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10.1016/j.bpc.2020.106510

http://scihub22266oqcxt.onion/10.1016/j.bpc.2020.106510
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33285430!7695570!33285430
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suck abstract from ncbi

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  • An insight into the interaction between alpha-ketoamide- based inhibitor and coronavirus main protease: A detailed in silico study #MMPMID33285430
  • Banerjee S
  • Biophys Chem 2021[Feb]; 269 (ä): 106510 PMID33285430show ga
  • The search for therapeutic drugs that can neutralize the effects of COVID-2019 (SARS-CoV-2) infection is the main focus of current research. The coronavirus main protease (Mpro) is an attractive target for anti-coronavirus drug design. Further, alpha-ketoamide is proved to be very effective as a reversible covalent-inhibitor against cysteine proteases. Herein, we report on the non-covalent to the covalent adduct formation mechanism of alpha-ketoamide-based inhibitor with the enzyme active site amino acids by QM/SQM model (QM = quantum mechanical, SQM = semi-empirical QM). To uncover the mechanism, we focused on two approaches: a concerted and a stepwise fashion. The concerted pathway proceeds via deprotonation of the thiol of cysteine (here, Cys145 SgammaH) and simultaneous reversible nucleophilic attack of sulfur onto the alpha-ketoamide warhead. In this work, we propose three plausible concerted pathways. On the contrary, in a traditional two-stage pathway, the first step is proton transfer from Cys145 SgammaH to His41 Ndelta forming an ion pair, and consecutively, in the second step, the thiolate ion attacks the alpha-keto group to form a thiohemiketal. In this reaction, we find that the stability of the tetrahedral intermediate oxyanion/hydroxyl group plays an important role. Moreover, as the alpha-keto group has two faces Si or Re for the nucleophilic attack, we considered both possibilities of attack leading to S- and R-thiohemiketal. We computed the structural, electronic, and energetic parameters of all stationary points including transition states via ONIOM and pure DFT method. Additionally, to characterize covalent, weak noncovalent interaction (NCI) and hydrogen-bonds, we applied NCI-reduced density gradient (NCI-RDG) methods along with Bader's Quantum Theory of Atoms-in-Molecules (QTAIM) and natural bonding orbital (NBO) analysis.
  • |Amides/*chemistry/metabolism[MESH]
  • |Binding Sites[MESH]
  • |Catalytic Domain[MESH]
  • |Coronavirus Infections/pathology/virology[MESH]
  • |Coronavirus M Proteins/antagonists & inhibitors/metabolism[MESH]
  • |Coronavirus/*enzymology/isolation & purification[MESH]
  • |Drug Design[MESH]
  • |Humans[MESH]
  • |Hydrogen Bonding[MESH]
  • |Molecular Docking Simulation[MESH]
  • |Peptide Hydrolases/*chemistry/metabolism[MESH]
  • |Protease Inhibitors/*chemistry/metabolism[MESH]
  • |Quantum Theory[MESH]
  • |Thermodynamics[MESH]
  • |Viral Proteins/*antagonists & inhibitors/metabolism[MESH]


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  • suck abstract from ncbi

    106510 ä.269 2021