Table 4.
Docking score and the interactions of the inhibitors with Host cell protease
| Ligands | Binding Affinity ΔG (Kcal/mol) | Inhibition Constant Ki (µM) 10–6 |
Interacting Amino acids | Bond Type |
|---|---|---|---|---|
| Lopinavir | − 8.0 | 1.7 | ALA 281, GLY 282, ARG 130, ALA 284, GLN 283, ILE 363, TYR 52, PRO 50, TRP 73, PRO 53, LEU 51, PHE 66, VAL 65, ILE 135, LYS 68, LEU 132 | Van der waals, Conventional Hydrogen Bond, Carbon Hydrogen Bond, Pi-Sigma, P-i-Pi Stacked, Alkyl, Pi-Alkyl |
| Dexamethasone | − 7.3 | 5.4 | GLY 378, HIS 203, SER 353, SER 376 | Conventional Hydrogen Bond, Pi-Alkyl |
| Merimepodib | − 7.2 | 6.3 | TYR 52, PHE 66, LEU 51, PRO 53, PRO 50, ILE 363 | Carbon Hydrogen Bond, Pi-Sigma, Pi-Pi Stacked, Alkyl, Pi-Alkyl |
| Remdesivir | − 7.1 | 7.5 | SER 353, SER 376, VAL 375, GLY 380, GLY 378, CYS 381, ALA 348, CYS 349, TRP 377, GLN 350, TYR 301, ASN 254, SER 251, ARG 208, PRO 245, ASN 250, PRO 206, TYR 243, HIS 203, GLY 351 | Van der waals, Conventional Hydrogen Bond, Unfavorable Positive-Positive Amide-Pi Stacked, Pi-Alkyl |
| Ritonavir | − 7.1 | 7.5 | HIS 186, GLN 350, HIS 203, ARG 208, PRO 206, PHE 246, ASN 250, PRO 245, TYR 243, TYR 301, ASN 254, SER 353, TRP 377, SER 376, GLY 378, GLY 380, VAL 375, CYS 381, CYS 349, ALA 348, ASN 298, GLY 351, LEU 187, GLN 305 | Van der waals, Conventional Hydrogen Bond, Carbon Hydrogen Bond, Unfavorable Donor-Donor, Pi-Cation, Pi-Pi T-shaped, Alkyl, Pi-Alkyl |
| Favipiravir | − 6.1 | 39.3 | CYS 349, TRP 377, ALA 348, CYS 381, ALA 348, GLY 380, GLY 378, GLN 350, SER 376, HIS 203, GLY 351, SER 353, VAL 375, GLY 388, VAL 389, ASP 347 | Van der waals, Conventional Hydrogen Bond, Carbon Hydrogen Bond, Unfavorable Donor-Donor, Amide-Pi Stacked, Pi-Alkyl |
| EIDD-2801 | − 5.8 | 64.8 | HIS 203, GLY 351, CYS 188, LEU 187, SER 353, GLN 350, VAL 375, GLY 388, VAL 389, ALA 348, CYS 349, GLY 380, CYS 381, GLY 378, TRP 377, SER 376 | Van der waals, Conventional Hydrogen Bond, Carbon Hydrogen Bond |
| Hydroxychloroquine | − 4.8 | 342.0 | GLN 305, ASN 298, GLN 350, TYR 301, TYR 302, ASN 209, TYR 182, ALA 185, LEU 185, HIS 186 | Van der waals, Convnetional Hydrogen Bond, Carbon Hydrogen Bond, Unfavorable Acceptor-Acceptor, Pi-Sigma, Pi-Alkyl |