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Literature summary for 3.4.22.B80 extracted from

  • Rao, P.; Patel, R.; Shukla, A.; Parmar, P.; Rawal, R.; Saraf, M.; Goswami, D.
    Identifying structural-functional analogue of GRL0617, the only well-established inhibitor for papain-like protease (PLpro) of SARS-CoV2 from the pool of fungal metabolites using docking and molecular dynamics simulation (2022), Mol. Divers., 26, 309-329 .
    View publication on PubMedView publication on EuropePMC
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Inhibitors

Inhibitors Comment Organism Structure
5-amino-2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]benzamide i.e. GRL0617, binding free energy -67.06 kcal/mol. Most contacts between SARS-CoV PLpro and inhibitor GRL0617 are hydrophobic in nature. The 1-naphthyl group is partly solvent-exposed but forms hydrophobic interactions with the aromatic rings of Tyr265 and Tyr269 and with the side chains of Pro248 and Pro249 severe acute respiratory syndrome coronavirus
5-amino-2-methyl-N-[(1R)-1-(naphthalen-1-yl)ethyl]benzamide i.e. GRL0617, binding free energy -63.12 kcal/mol. Most contacts between SARS-CoV-2 PLpro and inhibitor GRL0617 are hydrophobic in nature. The 1-naphthyl group is partly solvent-exposed but forms hydrophobic interactions with the aromatic rings of Tyr264 and Tyr268 and with the side chains of Pro248 Severe acute respiratory syndrome coronavirus 2
flaviolin binding energy -6.55 kcal/mol, binding free energy -32.66 kcal/mol, effective binding with Tyr269 for SARS-CoV PLpro has multiple types of interactions with amino acids and shows binding energy close to or at par with GRL0617 severe acute respiratory syndrome coronavirus
flaviolin binding free energy -30.45 kcal/mol, effective binding with Tyr 268 for SARS-CoV-2 PLprohas multiple types of interactions with amino acids and shows binding energy close to or at par with GRL0617 Severe acute respiratory syndrome coronavirus 2
fonsecin binding energy -7.25 kcal/mol, binding free energy -54.22 kcal/mol, effective binding with Tyr269 for SARS-CoV PLpro has multiple types of interactions with amino acids and shows binding energy close to or at par with GRL0617 severe acute respiratory syndrome coronavirus
fonsecin binding free energy -50.82 kcal/mol, effective binding with Tyr 268 for SARS-CoV-2 PLprohas multiple types of interactions with amino acids and shows binding energy close to or at par with GRL0617 Severe acute respiratory syndrome coronavirus 2
nigerloxin binding energy -6.62 kcal/mol, binding free energy -37.34 kcal/mol, effective binding with Tyr269 for SARS-CoVPL pro has multiple types of interactions with amino acids and shows binding energy close to or at par with GRL0617 severe acute respiratory syndrome coronavirus
nigerloxin binding free energy -35.56 kcal/mol, effective binding with Tyr 268 for SARS-CoV-2 PLprohas multiple types of interactions with amino acids and shows binding energy close to or at par with GRL0617 Severe acute respiratory syndrome coronavirus 2
ochratoxin beta binding energy -6.03 kcal/mol, binding free energy -34.54 kcal/mol, effective binding with Tyr269 for SARS-CoV PLpro has multiple types of interactions with amino acids and shows binding energy close to or at par with GRL0617 severe acute respiratory syndrome coronavirus
ochratoxin beta binding free energy -30.63 kcal/mol, effective binding with Tyr 268 for SARS-CoV-2 PLprohas multiple types of interactions with amino acids and shows binding energy close to or at par with GRL0617 Severe acute respiratory syndrome coronavirus 2
pyranonigrin-B binding energy -6.76 kcal/mol, binding free energy -24.64 kcal/mol, effective binding with Tyr269 for SARS-CoVPL pro has multiple types of interactions with amino acids and shows binding energy close to or at par with GRL0617 severe acute respiratory syndrome coronavirus
pyranonigrin-B binding free energy -26.43 kcal/mol, effective binding with Tyr 268 for SARS-CoV-2 PLprohas multiple types of interactions with amino acids and shows binding energy close to or at par with GRL0617 Severe acute respiratory syndrome coronavirus 2
tensidol A binding energy -6.34 kcal/mol, binding free energy -29.32 kcal/mol, effective binding with Tyr269 for SARS-CoV PLpro has multiple types of interactions with amino acids and shows binding energy close to or at par with GRL0617 severe acute respiratory syndrome coronavirus
tensidol A binding free energy -28.21 kcal/mol, effective binding with Tyr 268 for SARS-CoV-2 PLprohas multiple types of interactions with amino acids and shows binding energy close to or at par with GRL0617 Severe acute respiratory syndrome coronavirus 2

Organism

Organism UniProt Comment Textmining
severe acute respiratory syndrome coronavirus P0C6U8 replicase polyprotein 1a
-
Severe acute respiratory syndrome coronavirus 2 P0DTD1 replicase polyprotein 1ab
-