Predicted antiviral drugs Darunavir, Amprenavir, Rimantadine and Saquinavir can potentially bind to neutralize SARS-CoV-2 conserved proteins

Halder, Umesh C.

doi:10.1186/s40709-021-00149-2

Journal of Biological Research-Thessaloniki

Table 11 Possible binding sites of NSP16-NSP10 complex against known anti-viral drugs

From: Predicted antiviral drugs Darunavir, Amprenavir, Rimantadine and Saquinavir can potentially bind to neutralize SARS-CoV-2 conserved proteins

Drugs		Total binding sites			(7BQ7) NSP16-NSP10 complex of COVID-19
Amprenavir	Known similar target molecule				Protease, HIV-1
	Binding properties	2	1	Superposition type	L
				RMSD	0.54 Å
				Amino acid targets of drug	106 ASP 70 GLY 71 ALA
				No. of residues in known binding	18
				Human similar targets	4
			2	Superposition type	L
				RMSD	0.96 Å
				Amino acid targets of drug	157 ILE 208 GLY 207 ILE
				No. of residues in known binding	24
				Human similar targets	6
Atazanavir	Known similar target molecule				Protease, HIV-1
	Binding properties	3	1	Superposition type	R
				RMSD	0.94 Å
				Amino acid targets of drug	107 PRO 108 VAL 38 ILE
				No. of residues in known binding	19
				Human similar targets	4
			2	Superposition type	L
				RMSD	0.92 Å
				Amino acid targets of drug	78 ARG 107 PRO 108 VAL
				No. of residues in known binding	23
				Human similar targets	3
			3	Superposition type	L
				RMSD	0.88 Å
				Amino acid targets of drug	97 ASP 107 ALA 108 ASP
				No. of residues in known binding	18
				Human similar targets	3
Darunavir	Known similar target molecule				Protease, HIV-1
	Binding properties	5	1	Superposition type	L
				RMSD	0.54 Å
				Amino acid targets of drug	106 ASP 70 GLY 71 ALA
				No. of residues in known binding	27
				Human similar targets	7
			2	Superposition type	R
				RMSD	0.95 Å
				Amino acid targets of drug	78 ARG 107 PRO 108 VAL
				No. of residues in known binding	21
				Human similar targets	6
			3	Superposition type	R
				RMSD	0.93 Å
				Amino acid targets of drug	26 ALA 22 ASP 21 VAL
				No. of residues in known binding	21
				Human similar targets	6
			4	Superposition type	R
				RMSD	0.87 Å
				Amino acid targets of drug	121 ALA 290 ILE 288 VAL
				No. of residues in known binding	19
				Human similar targets	13
			5	Superposition type	L
				RMSD	1.00 Å
				Amino acid targets of drug	85 LEU 96 VAL 67 VAL
				No. of residues in known binding	22
				Human similar targets	6
Grazoprevir	Known similar target molecule				Protease, HIV-1
	Binding properties	2	1	Superposition type	R
				RMSD	1.02 Å
				Amino acid targets of drug	55 ILE 95 LYS 94 GLY
				No. of residues in known binding	16
				Human similar targets	8
			2	Superposition type	R
				RMSD	1.09 Å
				Amino acid targets of drug	119 HIS 294 VAL 293 ASP
				No. of residues in known binding	17
				Human similar targets	8
Indinavir	Known similar target molecule				Polyprotein, HIV-1
	Binding properties	1	1	Superposition type	L
				RMSD	0.94 Å
				Amino acid targets of drug	78 ARG 107 PRO 108 VAL
				No. of residues in known binding	24
				Human similar targets	2
Lopinavir	Known similar target molecule				Protease, HIV-1
	Binding properties	1	1	Superposition type	L
				RMSD	0.84 Å
				Amino acid targets of drug	78 ARG 107 PRO 108 VAL
				No. of residues in known binding	23
				Human similar targets	6
Nelfinavir	Known similar target molecule				Protease, HIV-1
	Binding properties	1	1	Superposition type	L
				RMSD	0.50 Å
				Amino acid targets of drug	106 ASP 70 GLY 71 ALA
				No. of residues in known binding	30
				Human similar targets	8
Rimantadine	Known similar target molecule				M2 protein, Influeza A
	Binding properties	2	1	Superposition type	R
				RMSD	0.86 Å
				Amino acid targets of drug	197 VAL 199 ALA 200 SER
				No. of residues in known binding	10
				Human similar targets	0
			2	Superposition type	L
				RMSD	0.93 Å
				Amino acid targets of drug	32 ALA 33 SER 34 GLY
				No. of residues in known binding	9
				Human similar targets	0
Ritonavir	Known similar target molecule				Protease, HIV-1
	Binding properties	2	1	Superposition type	L
				RMSD	0.77 Å
				Amino acid targets of drug	97 ASP 107 ALA 108 ASP
				No. of residues in known binding	18
				Human similar targets	4
			2	Superposition type	L
				RMSD	0.98 Å
				Amino acid targets of drug	78 ARG 107 PRO 108 VAL
				No. of residues in known binding	23
				Human similar targets	4
Saquinavir	Known similar target molecule				Protease, HIV-1
	Binding properties	4	1	Superposition type	L
				RMSD	1.02 Å
				Amino acid targets of drug	157 ILE 208 GLY 207 ILE
				No. of residues in known binding	29
				Human similar targets	7
			2	Superposition type	R
				RMSD	1.01 Å
				Amino acid targets of drug	257 THR 62 PRO 61 VAL
				No. of residues in known binding	22
				Human similar targets	4
			3	Superposition type	L
				RMSD	0.80 Å
				Amino acid targets of drug	78 ARG 107 PRO 108 VAL
				No. of residues in known binding	31
				Human similar targets	8
			4	Superposition type	L
				RMSD	0.52 Å
				Amino acid targets of drug	106 ASP 70 GLY 71 ALA
				No. of residues in known binding	31
				Human similar targets	7
Tipranavir	Known similar target molecule				Protease, HIV-1
	Binding properties	1	1	Superposition type	L
				RMSD	0.53 Å
				Amino acid targets of drug	106 ASP 70 GLY 71 ALA
				No. of residues in known binding	27
				Human similar targets	7

Features of different drug binding motifs. HIV-1 Human Immunodeficiency virus 1, RMSD Root Mean Square Deviation, Å angstrom, ILE isoleucine, GLY glycine, VAL valine, LEU leucine, PRO proline, ASP aspartic acid

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ISSN: 2241-5793

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