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10.1021/acs.biochem.0c00782 http://scihub22266oqcxt.onion/10.1021/acs.biochem.0c00782 33205654!7688048!33205654     free     free     free Warning: file_get_contents(https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=33205654&cmd=llinks): Failed to open stream: HTTP request failed! 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Exploring the Mechanism of Covalent Inhibition: Simulating the Binding Free Energy of alpha-Ketoamide Inhibitors of the Main Protease of SARS-CoV-2 |pdf=|usr=}}{{33205654}} gab.com Text Exploring the Mechanism of Covalent Inhibition: Simulating the Binding Free Energy of alpha-Ketoamide Inhibitors of the Main Protease of SARS-CoV-2 JO: Biochemistry http://www.kidney.de/pget.php?&tw=1&pmid=33205654 #FOAvip The development of reliable ways of predicting the binding free energies of covalent inhibitors is a challenge for computer-aided drug design. Such development is important, for example, in the fight against the SARS-CoV-2 virus, in which covalent inhibitors can provide a promising tool for blocking M(pro), the main protease of the virus. This work develops a reliable and practical protocol for evaluating the binding free energy of covalent inhibitors. Our protocol presents a major advance over other approaches that do not consider the chemical contribution of the binding free energy. Our strategy combines the empirical valence bond method for evaluating the reaction energy profile and the PDLD/S-LRA/beta method for evaluating the noncovalent part of the binding process. This protocol has been used in the calculations of the binding free energy of an alpha-ketoamide inhibitor of M(pro). Encouragingly, our approach reproduces the observed binding free energy. Our study of covalent inhibitors of cysteine proteases indicates that in the choice of an effective warhead it is crucial to focus on the exothermicity of the point on the free energy surface of a peptide cleavage that connects the acylation and deacylation steps. Overall, we believe that our approach should provide a powerful and effective method for in silico design of covalent drugs. Twit Text FOAVip Exploring the Mechanism of Covalent Inhibition: Simulating the Binding Free Energy of alpha-Ketoamide Inhibitors of the Main Protease of SARS-CoV-2 ????Biochemistry http://www.kidney.de/pget.php?&tw=1&pmid=33205654 #FOAvip Twit Text # Free Paper on # # # # # LINK http://www.kidney.de/pget.php?&tw=1&pmid=33205654 #FOAvip English Wikipedia <ref>{{Cite pmid|33205654}}</ref> Exploring the Mechanism of Covalent Inhibition: Simulating the Binding Free Energy of alpha-Ketoamide Inhibitors of the Main Protease of SARS-CoV-2 #MMPMID33205654 Mondal D; Warshel A Biochemistry 2020[Dec]; 59 (48): 4601-4608 PMID33205654show ga The development of reliable ways of predicting the binding free energies of covalent inhibitors is a challenge for computer-aided drug design. Such development is important, for example, in the fight against the SARS-CoV-2 virus, in which covalent inhibitors can provide a promising tool for blocking M(pro), the main protease of the virus. This work develops a reliable and practical protocol for evaluating the binding free energy of covalent inhibitors. Our protocol presents a major advance over other approaches that do not consider the chemical contribution of the binding free energy. Our strategy combines the empirical valence bond method for evaluating the reaction energy profile and the PDLD/S-LRA/beta method for evaluating the noncovalent part of the binding process. This protocol has been used in the calculations of the binding free energy of an alpha-ketoamide inhibitor of M(pro). Encouragingly, our approach reproduces the observed binding free energy. Our study of covalent inhibitors of cysteine proteases indicates that in the choice of an effective warhead it is crucial to focus on the exothermicity of the point on the free energy surface of a peptide cleavage that connects the acylation and deacylation steps. Overall, we believe that our approach should provide a powerful and effective method for in silico design of covalent drugs. |Amides/*chemistry/metabolism/*pharmacology[MESH] |Molecular Docking Simulation[MESH] |Peptide Hydrolases/chemistry/*metabolism[MESH] |Protease Inhibitors/*chemistry/metabolism/*pharmacology[MESH] |Protein Binding[MESH] |Protein Conformation[MESH] |SARS-CoV-2/drug effects/*enzymology[MESH]Exploring the Mechanism of Covalent Inhibition: Simulating the Binding(epmc).pdf DeepDyve Pubget Overpricing