Computational Evaluation of the Inhibition Efficacies of HIV Antivirals on SARS-CoV-2 (COVID-19) Protease and Identification of 3D Pharmacophore and Hit Compounds

Table 2

Binding scores and nature of interactions of J4-1 and J4-2 group molecules on the SARS-CoV-2 protease.

Pharmacophore	ZINC ID	Binding energy (kcal/mol)	Interactions	Amino acid residues
J4-1	38143759	−8.5	H-bond	His41(HB), Thr26(NC)
			π type	Cys145(π-R), Met165-2(π-R)
			Unfavourable	Gly143(π-R)
	67903263	−8.4	H-bond	Asn142-2(HB), Thr26(NC), Leu141(NC)
			π type	Met165-2(π-R), Cys145(π-R)
			Unfavourable	Thr190
J4-2	16384777	−8.1	H-bond	Gly143(HB), Cys145(HB), Thr25(HB), Met165(NC)
			π type	His41(π-stack), Met49(π-R), Met49(R), Met165(π-S)
			Unfavourable	Asn142, Ser144
	32953984	−8.4	H-bond	Glu166(HB), His164(HB), Gln189(HB)
			π type	Met165(π-S), Leu167(R), Pro168(R), Met165(R), His41(π-stack), His41(π^+), Cys145-2(π-S), Met49(π-R), Pro168(π-R), Met165(π-sigma)
	33130718	−8.3	H-bond	Gln189(HB), Gu166(HB), His164(HB)
			π type	Met165-2(π-S), Cys145-2(π-S), Pro168(π-R), His41(π-stack), His41(π^+), Met49(π-R)
	33130747	−8.3	H-bond	Glu166(HB), His164(HB), Gln189(HB), Arg188(NC), Gln189(NC)
			π type	Met165(π-sigma), Met49(π-R),Cys145-2(π-S), Pro168(π-R)
	33130768	−8.6	H-bond	Glu166(HB), Gln189(HB), His164(HB)
			π type	Cys145-2(π-S), Met165(π-sigma), Met165(π-S), His41(π-stack), His41(π^+), Pro168(π-R)
			Halogen(F)	Glu166(F)