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10.1080/07391102.2020.1768149 http://scihub22266oqcxt.onion/10.1080/07391102.2020.1768149 32396767!7284146!32396767     free     free     free Deprecated: Implicit conversion from float 211.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 211.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 211.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 211.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 211.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 211.6 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 245.2 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 245.2 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 245.2 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 245.2 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 245.2 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534 Deprecated: Implicit conversion from float 245.2 to int loses precision in C:\Inetpub\vhosts\kidney.de\httpdocs\pget.php on line 534       J+Biomol+Struct+Dyn 2021 ; 39 (10): 3649-3661 Nephropedia Template TP {{tp|p=32396767|t=2021. Elucidating biophysical basis of binding of inhibitors to SARS-CoV-2 main protease by using molecular dynamics simulations and free energy calculations |pdf=|usr=}}{{32396767}} gab.com Text Elucidating biophysical basis of binding of inhibitors to SARS-CoV-2 main protease by using molecular dynamics simulations and free energy calculations JO: J Biomol Struct Dyn http://www.kidney.de/pget.php?&tw=1&pmid=32396767 #FOAvip The recent outbreak of novel "coronavirus disease 2019" (COVID-19) has spread rapidly worldwide, causing a global pandemic. In the present work, we have elucidated the mechanism of binding of two inhibitors, namely alpha-ketoamide and Z31792168, to SARS-CoV-2 main protease (M(pro) or 3CL(pro)) by using all-atom molecular dynamics simulations and free energy calculations. We calculated the total binding free energy (DeltaG(bind)) of both inhibitors and further decomposed DeltaG(bind) into various forces governing the complex formation using the Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) method. Our calculations reveal that alpha-ketoamide is more potent (DeltaG(bind)= - 9.05 kcal/mol) compared to Z31792168 (DeltaG(bind)= - 3.25 kcal/mol) against COVID-19 3CL(pro). The increase in DeltaG(bind) for alpha-ketoamide relative to Z31792168 arises due to an increase in the favorable electrostatic and van der Waals interactions between the inhibitor and 3CL(pro). Further, we have identified important residues controlling the 3CL(pro)-ligand binding from per-residue based decomposition of the binding free energy. Finally, we have compared DeltaG(bind) of these two inhibitors with the anti-HIV retroviral drugs, such as lopinavir and darunavir. It is observed that alpha-ketoamide is more potent compared to lopinavir and darunavir. In the case of lopinavir, a decrease in van der Waals interactions is responsible for the lower binding affinity compared to alpha-ketoamide. On the other hand, in the case of darunavir, a decrease in the favorable intermolecular electrostatic and van der Waals interactions contributes to lower affinity compared to alpha-ketoamide. Our study might help in designing rational anti-coronaviral drugs targeting the SARS-CoV-2 main protease.Communicated by Ramaswamy H. Sarma. Twit Text FOAVip Elucidating biophysical basis of binding of inhibitors to SARS-CoV-2 main protease by using molecular dynamics simulations and free energy calculations ????J Biomol Struct Dyn http://www.kidney.de/pget.php?&tw=1&pmid=32396767 #FOAvip Twit Text # Free Paper on # # # # # LINK http://www.kidney.de/pget.php?&tw=1&pmid=32396767 #FOAvip English Wikipedia <ref>{{Cite pmid|32396767}}</ref> Elucidating biophysical basis of binding of inhibitors to SARS-CoV-2 main protease by using molecular dynamics simulations and free energy calculations #MMPMID32396767 Sk MF; Roy R; Jonniya NA; Poddar S; Kar P J Biomol Struct Dyn 2021[Jul]; 39 (10): 3649-3661 PMID32396767show ga The recent outbreak of novel "coronavirus disease 2019" (COVID-19) has spread rapidly worldwide, causing a global pandemic. In the present work, we have elucidated the mechanism of binding of two inhibitors, namely alpha-ketoamide and Z31792168, to SARS-CoV-2 main protease (M(pro) or 3CL(pro)) by using all-atom molecular dynamics simulations and free energy calculations. We calculated the total binding free energy (DeltaG(bind)) of both inhibitors and further decomposed DeltaG(bind) into various forces governing the complex formation using the Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) method. Our calculations reveal that alpha-ketoamide is more potent (DeltaG(bind)= - 9.05 kcal/mol) compared to Z31792168 (DeltaG(bind)= - 3.25 kcal/mol) against COVID-19 3CL(pro). The increase in DeltaG(bind) for alpha-ketoamide relative to Z31792168 arises due to an increase in the favorable electrostatic and van der Waals interactions between the inhibitor and 3CL(pro). Further, we have identified important residues controlling the 3CL(pro)-ligand binding from per-residue based decomposition of the binding free energy. Finally, we have compared DeltaG(bind) of these two inhibitors with the anti-HIV retroviral drugs, such as lopinavir and darunavir. It is observed that alpha-ketoamide is more potent compared to lopinavir and darunavir. In the case of lopinavir, a decrease in van der Waals interactions is responsible for the lower binding affinity compared to alpha-ketoamide. On the other hand, in the case of darunavir, a decrease in the favorable intermolecular electrostatic and van der Waals interactions contributes to lower affinity compared to alpha-ketoamide. Our study might help in designing rational anti-coronaviral drugs targeting the SARS-CoV-2 main protease.Communicated by Ramaswamy H. Sarma. |*Protease Inhibitors/pharmacology[MESH] |Coronavirus 3C Proteases/*antagonists & inhibitors[MESH] |Molecular Dynamics Simulation[MESH] |Peptide Hydrolases[MESH]Elucidating biophysical basis of binding of inhibitors to SARS-CoV-2 m(epmc).pdf DeepDyve Pubget Overpricing