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10.1016/j.compbiomed.2021.104295

http://scihub22266oqcxt.onion/10.1016/j.compbiomed.2021.104295
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suck abstract from ncbi


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pmid33662683      Comput+Biol+Med 2021 ; 131 (ä): 104295
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  • Targeting multiple conformations of SARS-CoV2 Papain-Like Protease for drug repositioning: An in-silico study #MMPMID33662683
  • Ismail MI; Ragab HM; Bekhit AA; Ibrahim TM
  • Comput Biol Med 2021[Apr]; 131 (ä): 104295 PMID33662683show ga
  • Papain-Like Protease (PLpro) is a key protein for SARS-CoV-2 viral replication which is the cause of the emerging COVID-19 pandemic. Targeting PLpro can suppress viral replication and provide treatment options for COVID-19. Due to the dynamic nature of its binding site loop, PLpro multiple conformations were generated through a long-range 1 micro-second molecular dynamics (MD) simulation. Clustering the MD trajectory enabled us to extract representative structures for the conformational space generated. Adding to the MD representative structures, X-ray structures were involved in an ensemble docking approach to screen the FDA approved drugs for a drug repositioning endeavor. Guided by our recent benchmarking study of SARS-CoV-2 PLpro, FRED docking software was selected for such a virtual screening task. The results highlighted potential consensus binders to many of the MD clusters as well as the newly introduced X-ray structure of PLpro complexed with a small molecule. For instance, three drugs Benserazide, Dobutamine and Masoprocol showed a superior consensus enrichment against the PLpro conformations. Further MD simulations for these drugs complexed with PLpro suggested the superior stability and binding of dobutamine and masoprocol inside the binding site compared to Benserazide. Generally, this approach can facilitate identifying drugs for repositioning via targeting multiple conformations of a crucial target for the rapidly emerging COVID-19 pandemic.
  • |*Coronavirus 3C Proteases/antagonists & inhibitors/chemistry[MESH]
  • |*Drug Repositioning[MESH]
  • |*Molecular Dynamics Simulation[MESH]
  • |Binding Sites[MESH]
  • |Crystallography, X-Ray[MESH]
  • |Cysteine Proteinase Inhibitors/*chemistry[MESH]
  • |Enzyme Stability[MESH]
  • |Humans[MESH]


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