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  • Rational approach toward COVID-19 main protease inhibitors via molecular docking, molecular dynamics simulation and free energy calculation #MMPMID33077821
  • Keretsu S; Bhujbal SP; Cho SJ
  • Sci Rep 2020[Oct]; 10 (1): 17716 PMID33077821show ga
  • In the rapidly evolving coronavirus disease (COVID-19) pandemic, repurposing existing drugs and evaluating commercially available inhibitors against druggable targets of the virus could be an effective strategy to accelerate the drug discovery process. The 3C-Like proteinase (3CL(pro)) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been identified as an important drug target due to its role in viral replication. The lack of a potent 3CL(pro) inhibitor and the availability of the X-ray crystal structure of 3CL(pro) (PDB-ID 6LU7) motivated us to perform computational studies to identify commercially available potential inhibitors. A combination of modeling studies was performed to identify potential 3CL(pro) inhibitors from the protease inhibitor database MEROPS ( ). Binding energy evaluation identified key residues for inhibitor design. We found 15 potential 3CL(pro) inhibitors with higher binding affinity than that of an alpha-ketoamide inhibitor determined via X-ray structure. Among them, saquinavir and three other investigational drugs aclarubicin, TMC-310911, and faldaprevir could be suggested as potential 3CL(pro) inhibitors. We recommend further experimental investigation of these compounds.
  • |*Molecular Docking Simulation[MESH]
  • |*Molecular Dynamics Simulation[MESH]
  • |Aclarubicin/chemistry/metabolism[MESH]
  • |Betacoronavirus/*enzymology/isolation & purification[MESH]
  • |Binding Sites[MESH]
  • |COVID-19[MESH]
  • |Coronavirus 3C Proteases[MESH]
  • |Coronavirus Infections/pathology/virology[MESH]
  • |Cysteine Endopeptidases/metabolism[MESH]
  • |Databases, Factual[MESH]
  • |Humans[MESH]
  • |Hydrogen Bonding[MESH]
  • |Oligopeptides/chemistry/metabolism[MESH]
  • |Pandemics[MESH]
  • |Pneumonia, Viral/pathology/virology[MESH]
  • |Protease Inhibitors/*chemistry/metabolism[MESH]
  • |SARS-CoV-2[MESH]
  • |Thermodynamics[MESH]
  • |Thiazoles/chemistry/metabolism[MESH]
  • |Viral Nonstructural Proteins/*antagonists & inhibitors/metabolism[MESH]

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  • suck abstract from ncbi

    17716 1.10 2020