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 9 Possible binding sites of NSP14 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			(5C8S) NSP14 of COVID-19
Amprenavir	Known similar target molecule				Protease, HIV-1
	Binding properties	3	1	Superposition type	R
				RMSD	0.83 Å
				Amino acid targets of drug	88 GLY 87 ILE 412 PRO
				No. of residues in known binding	24
				Human similar targets	4
			2	Superposition type	L
				RMSD	0.72 Å
				Amino acid targets of drug	170 LEU 162 VAL 166 ILE
				No. of residues in known binding	18
				Human similar targets	4
			3	Superposition type	L
				RMSD	0.87 Å
				Amino acid targets of drug	31 ILE 17 GLY 14 ILE
				No. of residues in known binding	24
				Human similar targets	6
Atazanavir	Known similar target molecule				Protease, HIV-1
	Binding properties	1	1	Superposition type	L
				RMSD	0.66 Å
				Amino acid targets of drug	78 ARG 107 PRO 108 VAL
				No. of residues in known binding	23
				Human similar targets	3
Darunavir	Known similar target molecule				Protease, HIV-1
	Binding properties	7	1	Superposition type	L
				RMSD	0.79 Å
				Amino acid targets of drug	88 GLY 87 ILE 412 PRO
				No. of residues in known binding	26
				Human similar targets	0
			2	Superposition type	L
				RMSD	1.38 Å
				Amino acid targets of drug	170 LEU 162 VAL 167 VAL 166 ILE
				No. of residues in known binding	26
				Human similar targets	7
			3	Superposition type	R
				RMSD	0.55 Å
				Amino acid targets of drug	78 ARG 107 PRO 108 VAL
				No. of residues in known binding	21
				Human similar targets	6
			4	Superposition type	L
				RMSD	0.79 Å
				Amino acid targets of drug	26 ALA 22 ASP 21 VAL
				No. of residues in known binding	27
				Human similar targets	7
			5	Superposition type	L
				RMSD	0.83 Å
				Amino acid targets of drug	435 ALA 390 ASP 389 VAL
				No. of residues in known binding	27
				Human similar targets	7
			6	Superposition type	R
				RMSD	0.94 Å
				Amino acid targets of drug	152 LEU 120 VAL 118 VAL
				No. of residues in known binding	20
				Human similar targets	6
			7	Superposition type	R
				RMSD	0.87 Å
				Amino acid targets of drug	508 LEU 317 VAL 312 VAL
				No. of residues in known binding	20
				Human similar targets	6
Grazoprevir	Known similar target molecule				NS3, NS4 Protease, Hepacivirus C
	Binding properties	1	1	Superposition type	L
				RMSD	0.90 Å
				Amino acid targets of drug	65 GLN 52 GLY 127 GLY
				No. of residues in known binding	17
				Human similar targets	7
Indinavir	Known similar target molecule				Polyprotein, HIV-1
	Binding properties	1	1	Superposition type	L
				RMSD	0.82 Å
				Amino acid targets of drug	78 ARG 107 PRO 108 VAL
				No. of residues in known binding	24
				Human similar targets	1
Lopinavir	Known similar target molecule				Protease, HIV-1
	Binding properties	2	1	Superposition type	R
				RMSD	0.65 Å
				Amino acid targets of drug	78 ARG 107 PRO 108 VAL
				No. of residues in known binding	27
				Human similar targets	6
			2	Superposition type	R
				RMSD	0.94 Å
				Amino acid targets of drug	31 ILE 17 GLY 14 ILE
				No. of residues in known binding	27
				Human similar targets	4
Rimantadine	Known similar target molecule				M2 protein, Influeza A
	Binding properties	5	1	Superposition type	L
				RMSD	0.86 Å
				Amino acid targets of drug	317 VAL 320 ALA 319 SER
				No. of residues in known binding	10
				Human similar targets	0
			2	Superposition type	L
				RMSD	0.90 Å
				Amino acid targets of drug	32 ALA 33 SER 34 GLY
				No. of residues in known binding	9
				Human similar targets	0
			3	Superposition type	L
				RMSD	0.80 Å
				Amino acid targets of drug	32 ALA 33 SER 35 GLY
				No. of residues in known binding	9
				Human similar targets	0
			4	Superposition type	R
				RMSD	0.67 Å
				Amino acid targets of drug	01 ALA 0 SER -1 GLY
				No. of residues in known binding	9
				Human similar targets	0
			5	Superposition type	R
				RMSD	0.91 Å
				Amino acid targets of drug	01 ALA 0 SER 102 GLY
				No. of residues in known binding	9
				Human similar targets	0
Saquinavir	Known similar target molecule				Protease, HIV-1
	Binding properties	2	1	Superposition type	L
				RMSD	0.90 Å
				Amino acid targets of drug	31 ILE 17 GLY 14 ILE
				No. of residues in known binding	21
				Human similar targets	4
			2	Superposition type	R
				RMSD	0.90 Å
				Amino acid targets of drug	84 ARG 244 VAL 277 THR
				No. of residues in known binding	29
				Human similar targets	9
Tipranavir	Known similar target molecule				Protease, HIV-1
	Binding properties	2	1	Superposition type	L
				RMSD	0.92 Å
				Amino acid targets of drug	274 ALA 273 ASP 90 ASP
				No. of residues in known binding	27
				Human similar targets	3
			2	Superposition type	L
				RMSD	1.25 Å
				Amino acid targets of drug	116 ASN 270 ALA 273 ASP 90 ASP
				No. of residues in known binding	18
				Human similar targets	2

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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