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Table 8 Possible binding sites of NSP13 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    (7NIO) NSP13 of COVID-19
Amprenavir Known similar target molecule Protease, HIV-1
Binding properties 3 1 Superposition type R
RMSD 0.81 Å
Amino acid targets of drug 258 ILE
294 GLY
293 ILE
No. of residues in known binding 24
Human similar targets 6
2 Superposition type L
RMSD 0.92 Å
Amino acid targets of drug 151 ILE
184 GLY
195 ILE
No. of residues in known binding 24
Human similar targets 6
3 Superposition type L
RMSD 0.76 Å
Amino acid targets of drug 226 VAL
184 GLY
195 ILE
No. of residues in known binding 18
Human similar targets 16
Atazanavir Known similar target molecule Protease, HIV-1
Binding properties 1 1 Superposition type L
RMSD 0.84 Å
Amino acid targets of drug 258 ILE
294 GLY
293 ILE
No. of residues in known binding 21
Human similar targets 3
Darunavir Known similar target molecule Protease, HIV-1
Binding properties 2 1 Superposition type L
RMSD 0.76 Å
Amino acid targets of drug 258 ILE
294 GLY
293 ILE
No. of residues in known binding 21
Human similar targets 6
2 Superposition type L
RMSD 0.72 Å
Amino acid targets of drug 226 VAL
184 GLY
195 ILE
No. of residues in known binding 22
Human similar targets 12
Indinavir Known similar target molecule Polyprotein, HIV-1
Binding properties 3 1 Superposition type L
RMSD 0.72 Å
Amino acid targets of drug 226 VAL
184 GLY
195 ILE
No. of residues in known binding 21
Human similar targets 3
2 Superposition type R
RMSD 0.92 Å
Amino acid targets of drug 399 ILE
400 GLY
282 GLY
No. of residues in known binding 22
Human similar targets 7
3 Superposition type L
RMSD 0.84 Å
Amino acid targets of drug 258 ILE
294 GLY
293 ILE
No. of residues in known binding 21
Human similar targets 6
Lopinavir Known similar target molecule Protease, HIV-1
Binding properties 2 1 Superposition type L
RMSD 0.84 Å
Amino acid targets of drug 258 ILE
294 GLY
293 ILE
No. of residues in known binding 27
Human similar targets 4
2 Superposition type L
RMSD 0.79 Å
Amino acid targets of drug 282 GLY
400 GLY
376 ILE
No. of residues in known binding 27
Human similar targets 6
Nelfinavir Known similar target molecule Protease, HIV-1
Binding properties 1 1 Superposition type L
RMSD 0.82 Å
Amino acid targets of drug 258 ILE
294 GLY
293 ILE
No. of residues in known binding 30
Human similar targets 9
Rimantadine Known similar target molecule M2 protein, Influeza A
Binding properties 2 1 Superposition type L
RMSD 0.88 Å
Amino acid targets of drug 01 ALA
13 SER
03 GLY
No. of residues in known binding 9
Human similar targets 0
2 Superposition type R
RMSD 0.84 Å
Amino acid targets of drug 522 ALA
523 SER
527 GLY
No. of residues in known binding 9
Human similar targets 0
Ritonavir Known similar target molecule Protease, HIV-1
Binding properties 1 1 Superposition type L
RMSD 0.82 Å
Amino acid targets of drug 258 ILE
294 GLY
293 ILE
No. of residues in known binding 18
Human similar targets 4
Saquinavir Known similar target molecule Protease, HIV-1
Binding properties 1 1 Superposition type R
RMSD 0.73 Å
Amino acid targets of drug 258 ILE
294 GLY
293 ILE
No. of residues in known binding 27
Human similar targets 3
Tipranavir Known similar target molecule Protease, HIV-1
Binding properties 1 1 Superposition type L
RMSD 0.87 Å
Amino acid targets of drug 258 ILE
294 GLY
293 ILE
No. of residues in known binding 27
Human similar targets 7
  1. 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