Table 3.
Ligand-driven molecular dynamics simulation data of ligands with best binding affinities recorded from docking study using explicit water model.
| P-L complex | RMSD (avg.) (Å) | Rg (Å) | ΔPBSAbind (kcal/mol) | ΔGBSAbind (kcal/mol) | H-bonding∗ | Dist. (Å) | Ang. (°) | |
|---|---|---|---|---|---|---|---|---|
| Ligand | Protein | |||||||
| Mpro | ||||||||
| Cryptospirolepine | 0.39 | 1.95 | 22.17 | -15.65 | -22.87 | Gly143, OH | 3.04 | 154.02 |
| Cryptomisirine | 0.51 | 1.74 | 22.19 | -14.32 | -24.37 | Arg188, N-H | 3.30 | 143.14 |
| Biscryptolepine | 0.60 | 1.43 | 22.14 | -12.68 | -21.16 | Gln189, N-H | 3.29 | 147.33 |
| Cryptoquindoline | 0.62 | 1.67 | 22.03 | -8.43 | -15.14 | Gln189, N-H | 3.27 | 153.77 |
| RdRp | ||||||||
| Cryptomisirine | 0.30 | 1.87 | 28.59 | -53.54 | -60.15 | Thr556, N-H | 3.06 | 152.95 |
| Cryptospirolepine | 0.68 | 1.85 | 28.76 | -44.94 | -54.45 | Asn691, N | 3.20 | 141.31 |
| Cryptoquindoline | 0.69 | 1.80 | 28.63 | -44.91 | -55.68 | Lys621, N-H | 3.33 | 151.55 |
| RemTP | 0.47 | 1.94 | 28.78 | 89.22 | 32.7 | Asp623, O-H | 3.07 | 149.90 |
| RdRpol | ||||||||
| Cryptospirolepine | 0.51 | 2.94 | 32.37 | -17.07 | -20.35 | Arg553, N-H | 3.27 | 143.58 |
| Cryptomisirine | 0.42 | 3.16 | 32.05 | -12.24 | -16.92 | Asp623, N-H | 3.13 | 151.01 |
| Cryptoquindoline | 0.47 | 2.99 | 38.65 | -4.98 | -10.66 | Lys621, N-H | 3.35 | 148.11 |
RMSD (avg): average root mean square deviation; Rg: average radius of gyration; ΔPBSA: binding free energy using Poisson-Boltzmann surface area continuum solvation; ΔGBSA: binding free energy Generalized Born surface area continuum solvation; H-bonding: most frequent interacting pocket residue; Dist.: average distance; Ang.: average interaction angle.