Table 3.

Non-covalent interactions of top ranked drugs with Mpro (PDB ID-6LU7) (Pose predicted by AutoDock Vina).

Drug candidate	Binding affinity	Hydrogen bond (AA…ligand)	Hydrophobic interaction (AA…ligand)	Electrostatic interaction (AA…ligand)	Other
Raltegravir	−9.1	HIS164(2.245) C-O…H-N	CYS145(5.309) Pi-Alkyl
		LEU141(2.803) C-O…H-O
		SER144(2.123) N-H…O-C
		SER144(2.463) O-H…O-C
		CYS145(2.244) N-H…O-C
		HIS163(3.0656) C-H…O-H
Simeprevir	−8.7	ASN142(1.875) N-H…O-S	MET165(4.338) Alkyl	GLU166(3.950) Pi-Anion
		ASN142(2.648) C-O…H-C	GLN189(2.557) Pi-Sigma
		THR26(2.926) C-O…H-C	MET49(3.910) Alkyl
		GLU166(3.042) C-O…H-C	LEU27(5.136) Alkyl
		GLU166(2.902) Pi-Donor	MET165(4.224) Pi-Alkyl
			HIS41(4.325) Pi-Alkyl
			HIS41 (4.662) Pi-Alkyl
Remdesivir	−7.8	ASN142(2.202) C-O…H-N	MET49(4.617) Pi-Alkyl		MET165(5.618) Pi-Sulfur
		PHE140(2.838) C-O…H-O
		GLU166(2.456) C-O…H-O
		HIS163(2.246) C-N…H-O
		GLY143(2.102) N-H…O-C
		HIS163(2.637) C-N…H-C
		LEU141(2.640) C-H…N-C
		ASN142(3.051) C-H…O-C
		HIS172(3.021) C-H…O-H
Cobicistat	−7.4	GLN189(2.571) C-O…H-N	MET49 (4.863) Alkyl		MET165(5.563) Pi-Sulfur
		GLN189(2.288) C-O…H-N	CYS145(4.230) Pi-Alkyl
		ASN142(2.650) N-H…O-C	MET49(4.644) Pi-Alkyl
		SER144(2.948) O-H…O-C
		GLU166(2.803) C-O…H-C
		GLN189(2.691) C-O…H-C
		ASN142(2.434) C-O…H-C
		PHE140(2.693) C-O…H-C
		GLN189(2.345) C-O…H-C
Daclatasvir	−7.2	ASN142(2.319) C-O…H-N	LEU50(4.214) Alkyl
		GLN189(2.677) C-O…H-N	LEU50(4.224) Alkyl
		SER144(2.537) O-H…O-C	CYS145(4.379) Alkyl
		HIS163(2.527) C-N…H-C	ALA191(4.919) Alkyl
		ASN142(2.437) C-O…H-C	ALA191(4.252) Pi-Alkyl
			HIS41(4.213) Pi-Alkyl