Computer-aided identification of a series of novel ligands showing high potency as hepatitis C virus NS3/4A protease inhibitors

Bulletin of the National Research Centre

Table 6 Docking results of Template molecule, designed molecule with the highest activity, first, second, and third generation approved direct-acting antiviral agents

The compound from Table 5	Binding energy kCal/mol	Residues interacting with ligand	Types of interaction	Bond length (Å)
1	− 7.5	THR298, SER229	Conventional Hydrogen Bond	2.17, 3.60
		SER297	Carbon Hydrogen Bond	3.69
		GLU291	Pi-Anion	3.51
		SER294, TRP501	Pi-Donor Hydrogen Bond	3.78, 3.54
		ALA497, PRO230, HIS293	Pi-Alkyl	4.48, 4.79, 5.48
7	− 10.7	THR416, THR416, SER294, THR295, GLY484	Conventional Hydrogen Bond	2.91, 2.79, 3.02, 2.85, 3.10
		TYR391, HIS293	Carbon Hydrogen Bond	3.70, 3.10
		ASP454	Pi-Anion	3.43
		SER457, THR295, SER483	Pi-Donor Hydrogen Bond	3.75, 4.05, 3.56
		ARG393, VAL456	Pi-Alkyl	4.69, 4.64
14	− 9.5	ARG481, MET485, GLY484, THR295, THR295, HIS369	Conventional Hydrogen Bond	3.18, 1.95, 3.11, 3.31, 3.10, 2.32
		VAL490, VAL490, PRO523, VAL456	Alkyl	4.99, 4.71, 4.34, 4.61
		VAL432	Pi-Alkyl	5.01
15	− 10.0	ALA413, GLN434	Conventional Hydrogen Bond	2.80, 3.21
		ASN556, SER489, GLU493	Carbon Hydrogen Bond	3.58, 3.14, 3.63
		ASP454	Pi-Anion	4.09
		THR295, THR433	Pi-Donor Hydrogen Bond	3.71, 3.88
		VAL456, VAL490	Alkyl	3.96, 3.57
		VAL456	Pi-Alkyl	4.93
16	− 10.5	GLU493, TRP501, TYR502, GLY253	Conventional Hydrogen Bond	2.39, 3.16, 2.50, 3.17
		THR269	Carbon Hydrogen Bond	3.47
		ASP412, ASP412	Halogen (Fluorine)	3.31, 3.40
		GLY271	Amide-Pi Stacked	4.59
		ALA413, PRO558	Alkyl	4.19, 4.50
		ALA497, TRP501	Pi-Alkyl	4.86, 5.06