Table 1 Interactions, distances and energy parameters of ligands in molecular docking with Mpro SRAS-CoV-2
Compound name | ΔG (kcal/mol) | Hydrogen bonding | ||
|---|---|---|---|---|
Atom of ligand | Amino acid | Distance (Å) | ||
Parental ligands | ||||
ART | − 6.2 | O sp2 | Lys102 | 2.96 |
ARA | − 6.7 | O sp2 | Arg131 | 3.02 |
O sp2 | Thr199 | 2.88 | ||
O sp2 | Thr199 | 3.16 | ||
O sp3 | Asn238 | 3.12 | ||
O sp2 | Tyr239 | 2.90 | ||
THY | − 4.08 | O sp2 | Tyr239 | 3.11 |
Artemisinin–thymoquinone hybrids | ||||
T1 | − 7.6 | O sp2 | Lys137 | 2.96 |
O sp2 | Thr199 | 2.94 | ||
O sp3 | Tyr239 | 3.15 | ||
T2 | − 7.5 | O sp2 | Lys137 | 3.04 |
O sp3 | Thr199 | 2.93 | ||
T3 | − 8.3 | O sp3 | Lys137 | 3.02 |
O sp2 | Lys137 | 3.06 | ||
O sp2 | Lys137 | 3.29 | ||
O sp2 | Thr199 | 2.86 | ||
O sp3 | Thr199 | 3.05 | ||
O sp3 | Thr199 | 3.17 | ||
O sp2 | Asn238 | 2.94 | ||
O sp3 | Tyr239 | 3.08 | ||
T4 | − 7.7 | O sp3 | Thr199 | 2.88 |
O sp2 | Asn238 | 3.17 | ||
T5 | − 7.8 | O sp2 | Asp197 | 3.31 |
O sp3 | Asn238 | 2.94 | ||
O sp3 | Tyr239 | 2.09 | ||
T6 | − 8.3 | O sp3 | Ser158 | 2.97 |
T7 | − 7.7 | – | – | – |
Control-ligands | ||||
ANK | − 6.2 | N sp2 | Lys137 | 3.35 |
O sp3 | Thr199 | 2.85 | ||
O sp2 | Thr199 | 2.93 | ||
N sp3 | Glu290 | 3.04 | ||
AZT | − 6.9 | O sp3 | Thr199 | 3.04 |
O sp3 | Tyr237 | 3.85 | ||
BRT | − 6.8 | N sp2 | Thr199 | 3.10 |
N arm | Leu287 | 3.10 | ||
CLQ | − 4.7 | – | – | – |
RDS | − 6.8 | O sp3 | Arg131 | 3.06 |
N sp3 | Asp197 | 3.31 | ||
Asn238 | 3.15 | |||
Tyr239 | 3.20 | |||
Leu287 | 3.14 | |||
Asp289 | 2.85 | |||