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10.1021/acs.jcim.0c00179

http://scihub22266oqcxt.onion/10.1021/acs.jcim.0c00179
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32315171!7197972!32315171
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suck abstract from ncbi


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pmid32315171      J+Chem+Inf+Model 2020 ; 60 (6): 3277-3286
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  • Fast Identification of Possible Drug Treatment of Coronavirus Disease-19 (COVID-19) through Computational Drug Repurposing Study #MMPMID32315171
  • Wang J
  • J Chem Inf Model 2020[Jun]; 60 (6): 3277-3286 PMID32315171show ga
  • The recent outbreak of novel coronavirus disease-19 (COVID-19) calls for and welcomes possible treatment strategies using drugs on the market. It is very efficient to apply computer-aided drug design techniques to quickly identify promising drug repurposing candidates, especially after the detailed 3D structures of key viral proteins are resolved. The virus causing COVID-19 is SARS-CoV-2. Taking advantage of a recently released crystal structure of SARS-CoV-2 main protease in complex with a covalently bonded inhibitor, N3 (Liu et al., 10.2210/pdb6LU7/pdb), I conducted virtual docking screening of approved drugs and drug candidates in clinical trials. For the top docking hits, I then performed molecular dynamics simulations followed by binding free energy calculations using an end point method called MM-PBSA-WSAS (molecular mechanics/Poisson-Boltzmann surface area/weighted solvent-accessible surface area; Wang, Chem. Rev. 2019, 119, 9478; Wang, Curr. Comput.-Aided Drug Des. 2006, 2, 287; Wang; ; Hou J. Chem. Inf. Model., 2012, 52, 1199). Several promising known drugs stand out as potential inhibitors of SARS-CoV-2 main protease, including carfilzomib, eravacycline, valrubicin, lopinavir, and elbasvir. Carfilzomib, an approved anticancer drug acting as a proteasome inhibitor, has the best MM-PBSA-WSAS binding free energy, -13.8 kcal/mol. The second-best repurposing drug candidate, eravacycline, is synthetic halogenated tetracycline class antibiotic. Streptomycin, another antibiotic and a charged molecule, also demonstrates some inhibitory effect, even though the predicted binding free energy of the charged form (-3.8 kcal/mol) is not nearly as low as that of the neutral form (-7.9 kcal/mol). One bioactive, PubChem 23727975, has a binding free energy of -12.9 kcal/mol. Detailed receptor-ligand interactions were analyzed and hot spots for the receptor-ligand binding were identified. I found that one hot spot residue, His41, is a conserved residue across many viruses including SARS-CoV, SARS-CoV-2, MERS-CoV, and hepatitis C virus (HCV). The findings of this study can facilitate rational drug design targeting the SARS-CoV-2 main protease.
  • |Anti-Bacterial Agents/chemistry/pharmacology[MESH]
  • |Betacoronavirus/chemistry/*drug effects/enzymology[MESH]
  • |COVID-19[MESH]
  • |Coronavirus 3C Proteases[MESH]
  • |Coronavirus Infections/*drug therapy/virology[MESH]
  • |Cysteine Endopeptidases/chemistry/metabolism[MESH]
  • |Drug Repositioning/economics/*methods[MESH]
  • |Humans[MESH]
  • |Molecular Docking Simulation[MESH]
  • |Molecular Dynamics Simulation[MESH]
  • |Oligopeptides/chemistry/pharmacology[MESH]
  • |Pandemics[MESH]
  • |Pneumonia, Viral/*drug therapy/virology[MESH]
  • |Protease Inhibitors/chemistry/*pharmacology[MESH]
  • |SARS-CoV-2[MESH]
  • |Tetracyclines/chemistry/pharmacology[MESH]
  • |Thermodynamics[MESH]
  • |Time Factors[MESH]


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