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10.1038/s41598-020-74099-5 http://scihub22266oqcxt.onion/10.1038/s41598-020-74099-5 33046764!7550358!33046764     free     free     free Deprecated: Implicit conversion from float 227.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 227.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 227.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 227.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 227.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 227.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 261.2 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534       Sci+Rep 2020 ; 10 (1): 16986 Nephropedia Template TP {{tp|p=33046764|t=2020. Drug binding dynamics of the dimeric SARS-CoV-2 main protease, determined by molecular dynamics simulation |pdf=|usr=}}{{33046764}} gab.com Text Drug binding dynamics of the dimeric SARS-CoV-2 main protease, determined by molecular dynamics simulation JO: Sci Rep http://www.kidney.de/pget.php?&tw=1&pmid=33046764 #FOAvip We performed molecular dynamics simulation of the dimeric SARS-CoV-2 (severe acute respiratory syndrome corona virus 2) main protease (M(pro)) to examine the binding dynamics of small molecular ligands. Seven HIV inhibitors, darunavir, indinavir, lopinavir, nelfinavir, ritonavir, saquinavir, and tipranavir, were used as the potential lead drugs to investigate access to the drug binding sites in M(pro). The frequently accessed sites on M(pro) were classified based on contacts between the ligands and the protein, and the differences in site distributions of the encounter complex were observed among the ligands. All seven ligands showed binding to the active site at least twice in 28 simulations of 200 ns each. We further investigated the variations in the complex structure of the active site with the ligands, using microsecond order simulations. Results revealed a wide variation in the shapes of the binding sites and binding poses of the ligands. Additionally, the C-terminal region of the other chain often interacted with the ligands and the active site. Collectively, these findings indicate the importance of dynamic sampling of protein-ligand complexes and suggest the possibilities of further drug optimisations. Twit Text FOAVip Drug binding dynamics of the dimeric SARS-CoV-2 main protease, determined by molecular dynamics simulation ????Sci Rep http://www.kidney.de/pget.php?&tw=1&pmid=33046764 #FOAvip Twit Text # Free Paper on # # # # # LINK http://www.kidney.de/pget.php?&tw=1&pmid=33046764 #FOAvip English Wikipedia <ref>{{Cite pmid|33046764}}</ref> Drug binding dynamics of the dimeric SARS-CoV-2 main protease, determined by molecular dynamics simulation #MMPMID33046764 Komatsu TS; Okimoto N; Koyama YM; Hirano Y; Morimoto G; Ohno Y; Taiji M Sci Rep 2020[Oct]; 10 (1): 16986 PMID33046764show ga We performed molecular dynamics simulation of the dimeric SARS-CoV-2 (severe acute respiratory syndrome corona virus 2) main protease (M(pro)) to examine the binding dynamics of small molecular ligands. Seven HIV inhibitors, darunavir, indinavir, lopinavir, nelfinavir, ritonavir, saquinavir, and tipranavir, were used as the potential lead drugs to investigate access to the drug binding sites in M(pro). The frequently accessed sites on M(pro) were classified based on contacts between the ligands and the protein, and the differences in site distributions of the encounter complex were observed among the ligands. All seven ligands showed binding to the active site at least twice in 28 simulations of 200 ns each. We further investigated the variations in the complex structure of the active site with the ligands, using microsecond order simulations. Results revealed a wide variation in the shapes of the binding sites and binding poses of the ligands. Additionally, the C-terminal region of the other chain often interacted with the ligands and the active site. Collectively, these findings indicate the importance of dynamic sampling of protein-ligand complexes and suggest the possibilities of further drug optimisations. |Betacoronavirus/*drug effects/metabolism[MESH] |Binding Sites/drug effects[MESH] |Biophysical Phenomena[MESH] |COVID-19[MESH] |Catalytic Domain/drug effects[MESH] |Computational Biology[MESH] |Coronavirus 3C Proteases[MESH] |Coronavirus Infections/*drug therapy[MESH] |Cysteine Endopeptidases/*metabolism[MESH] |Darunavir/metabolism/pharmacology[MESH] |Drug Repositioning/*methods[MESH] |HIV Protease Inhibitors/metabolism/*pharmacology[MESH] |Humans[MESH] |Indinavir/metabolism/pharmacology[MESH] |Lopinavir/metabolism/pharmacology[MESH] |Molecular Dynamics Simulation[MESH] |Nelfinavir/metabolism/pharmacology[MESH] |Pandemics[MESH] |Pneumonia, Viral/*drug therapy[MESH] |Ritonavir/metabolism/pharmacology[MESH] |SARS-CoV-2[MESH] |Saquinavir/metabolism/pharmacology[MESH]Drug binding dynamics of the dimeric SARS-CoV-2 main protease, determi(epmc).pdf DeepDyve Pubget Overpricing