Table 1.
Binding interactions between the alpha strain modelled spike protein and the ligands. The interactions are calculated using PLIP online server and Discovery Studio Visualizer for the docked complex.
| Ligand | Binding Energy (kcal/mol) | Hydrogen Bonds | VDW | Non-Covalent Interactions | Hydrophobic interactions |
|---|---|---|---|---|---|
| Ecamsule | -8.7 | Arg405 Gln406 |
Asp402, Glu403, Thr412, Gly413, Lys414, Ser491, Tyr492, Tyr502, Gly493, Tyr498, | 400Arg(π-cation) 405Arg (Saltbridge) 502Tyr(πstacking) |
402Asp,414Lys,450Tyr,492Tyr |
| Trypan Blue | -8.4 | Tyr450 Ser491 Tyr502 |
Tyr348,446,498 Asn447, Leu452, Glu490, Gly493 |
Leu449(π-sigma) Lys414, Arg400 |
446Tyr,449Leu, 490Gln,502Tyr |
| Digoxin | -8.3 | Tyr450 | NA | NA | Tyr 446,492 Leu492 |
| Naldemedine | -8.1 | Arg343 | Glu337, Ser396,346 Phe344, Ala345, Tyr348, Arg463, Asn351,447 |
Val338, Ala341,349, Lys353, Ile465 | Ala341,349 Arg343, Asn351 Lys353, Ile465 |
| Ergotamine | -7.9 | NA | NA | Phe487 | Ala349 Phe487 |
| Ponatinib | -7.9 | Asn447 Ser346 |
NA | Phe487(πstacking) Ala349, Leu449 Asn351, Phe344 Tyr348(halogen bond) |
Leu449, Phe487 |
| Conivaptan | -7.9 | NA | NA | Arg343, Tyr448, Leu449 |
Arg343, Asn447 Tyr448, Leu449 Phe487 |
| Orap | -7.9 | Arg343 Tyr446 Ser491 |
NA | Tyr448((π-(π) Ala345,349(π-sigma) Leu449 |
Arg343, Asn447 Tyr448, Leu449 Phe487 |
| Trosec | -7.8 | Tyr498 | NA | Tyr502(πstacked) | Tyr446,492, Tyr498,502 Gln490 |