Table 1.
Binding free energy components of complexes between ligands and SARS-CoV-2 spike protein (kcal/mol).
| Complex | ΔEvdw | ΔEele | ΔGele,sol | ΔGnpol,sol | ΔGmmgbsa |
|---|---|---|---|---|---|
| Cepharanthine | |||||
| D614G | − 32.15 (4.5) | − 11.43 (1.9) | 31.18 (8.0) | − 3.96 (0.50) | − 16.36 (3.7) |
| H49Y | − 32.15 (3.8) | − 1.9 (0.2) | 18.29 (6.0) | − 3.74 (0.30) | − 19.43 (3.3) |
| T573I | − 32.26 (5.9) | − 14.41 (0.4) | 31.68 (7.0) | − 3.83 (0.70) | − 18.83 (5.1) |
| WT | − 24.90 (4.0) | − 51.19 (11.0) | 63.53 (10.0) | − 2.97 (0.55) | − 15.53 (3.2) |
| Hydroxychloroquine | |||||
| D614G | ND | ND | ND | ND | ND |
| H49Y | − 18.43 (4.0) | − 15.05 (5.0) | 21.93 (5.0) | − 2.49 (0.40) | − 14.05 (3.7) |
| T573I | − 20.50 (4.0) | − 11.18 (1.0) | 18.87 (7.0) | − 2.71 (0.75) | − 15.53 (4.0) |
| WT | ND | ND | ND | ND | ND |
| Nelfinavir | |||||
| D614G | > 0 | ||||
| H49Y | − 23.42 (4.0) | − 66.49 (10.0) | 79.13 (10.0) | − 3.18 (0.50) | − 13.96 (3.6) |
| T573I | − 44.55 (3.0) | − 116.60 (12.0) | 127.29 (10.0) | − 5.47 (0.40) | − 39.34 (3.6) |
| WT | − 27.12 (3.6) | − 61.49 (9.0) | 72.38 (8.0) | − 3.29 (0.55) | − 19.52 (3.3) |
All energies are averaged over 200 snapshots at time intervals of 100 ps from the last 20 ns-long MD simulations, and they are in kcal/mol (± standard deviation). ND due to ligand diffuses of the binding pose at the first ns of simulations.