Table 1.

Docking score and the interactions of the inhibitors with PLpro

Ligands	Binding Affinity ΔG (Kcal/mol)	Inhibition Constant Ki (µM) 10–6	Interacting Amino acids	Bond type
Merimepodib	− 7.2	6.3	ASP 37, ALA 145, ALA 144, GLU 143, GLY 142, TRP 93, TYR 95, LYS 94, LYS 91, LEU 87, ASN 146, ARG 138, ALA 135, ASP 134, LEU 150, ALA 131, TYR 71, TYR 83, TYR 56, ASN 13	Van der waals, Conventional Hydrogen Bond, Carbon Hydrogen Bond, Pi-Anion, Alkyl, Pi-Alkyl
Dexamethasone	− 7.1	7.5	ASN 146, LEU 87, ALA 145, ALA 144, GLU 143, TRP 93, PRO 96, TYR 95, GLY 142, LYS 94, LYS 91	Van der waals, Conventional Hydrogen Bond, Unfavorable Donor-Donor, Halogen (Fluorine), Pi-Alkyl, Alkyl
Ritonavir	− 6.4	23.9	LYS 306, TYR 305, THR 257, TYR 251, GLY 256, PHE 258, THR 259, TYR 213, GLU 214, LYS 217, THR 313, TYR 310, LYS 218, GLU 307, ASN 308, SER 212	Van der waals, Conventional Hydrogen Bond, Carbon Hydrogen Bond, Pi-Anion, Amide-Pi Stacked, Alkyl, Pi-Alkyl
EIDD-2801	− 6.1	39.3	LYS 94, TYR 95, THR 90, TRP 93, LYS 91, GLU 143, ALA 145, ALA 144, ASN 146, ARG 138, ASN 146, GLY 142, PRO 96	Van der waals, Conventional Hydrogen Bond, Unfavorable Acceptor-Acceptor, Pi-Anion, Pi-Alkyl
Remdesvir	− 5.9	54.8	GLN 174, CYS 155, HIS 175, TYR 154, ALA 153, PHE 79, ARG 82, ASN 156, TYR 171, THR 74, THR 75, ASP 76, PRO 77	Van der waals, Attractive Charge, Conventional Hydrogen bond, Carbon hydrogen Bond, Pi-Pi T-shaped
Lopinavir	− 5.6	90.3	VA 188, TYR 233, THR 231, PRO 316, GLU 318, LEU 317, LYS 315, THR 313, ILE 314, LYS 218, GLY 219, GLN 215	Van der waals, Conventional Hydrogen Bond, Carbon Hydrogen Bond, Pi-Sigma, Alkyl, Pi-Alkyl
Favipiravir	− 5.5	107	LYS 254, TYR 251, GLU 252	Conventional Hydrogen Bond, Pi-Pi T-shaped, Pi-Alkyl
Hydroxychloroquine	− 4.7	403	SER 170, GLU 203, LEU 199. TYR 207, LYS 232, MET 208, MET 206, ARG 166, VAL 202	Van der waals, Conventional Hydrogen Bond, Pi-Sulfur, Pi-Alkyl, Alkyl