Table II.
Molecular interaction between SARS-CoV-2 Mpro and PLpro proteins with their respective inhibitors
| Hydrogen bonds | Hydrophobic interactions | Other residues making van der Waals’ interactions | Docking energy, ΔG [kcal/mol] | Docking affinity, Kd [M–1] | Ligand efficiency, LE [kcal/mol] |
|---|---|---|---|---|---|
| Mpro-proanthocyanidin complex | |||||
| Asn142, Cys145, His163, Glu166, Gln189, Thr190 |
Hie41 | Phe140, Leu141, Gly143, Ser144, His164, Met165, Leu167, Pro168, Hie172, Val186, Asp187, Arg188, Ala191, Gln192 |
–10.566 | 5.62 × 107 | –0.153 |
| PLpro-rhapontin complex | |||||
| Trp106, Gly271, Hie272, Asp286 |
Hie272 | Lys105, Asn109, Cys111, Leu162, Gln269, Cys270, Tyr273, Gly287, Ala288, Leu289 |
–10.022 | 2.24 × 107 | –0.186 |
The residues shown in bold are catalytic residues. Ligand efficiency (LE) was calculated using the relation LE = ΔG/N, where N is the number of non-hydrogen atoms in the ligand.