Structural Stability and Binding Ability of SARS-CoV-2 Main Protease with GC376: A Stereoisomeric Covalent Ligand Analysis by FMO calculation-Reference-Cited by-同舟云学术

Structural Stability and Binding Ability of SARS-CoV-2 Main Protease with GC376: A Stereoisomeric Covalent Ligand Analysis by FMO calculation

Published:2024-05-17 Issue:0 Volume:24 Page:13-24
ISSN:1347-0442
Container-title:Chem-Bio Informatics Journal
language:en
Short-container-title:CBIJ

Author:

Seki Yuya¹,Watanabe Chiduru²,Tani Norihiko²,Kamisaka Kikuko²,Ohyama Tatsuya³,Takaya Daisuke⁴,Honma Teruki²

Affiliation:

1. TechnoPro, Inc. TechnoPro R&D Company　Yokohama Branch

2. Center for Biosystems Dynamics Research, RIKEN

3. Frontier Institute for Biomolecular Engineering Research (FIBER), Konan University

4. Graduate School of Pharmaceutical Sciences, Osaka University

Funder

Research Support Project for Life Science and Drug Discovery (Basis for Supporting Innovative Drug Discovery and Life Science Research (BINDS)) from AMED

Publisher

Chem-Bio Informatics Society

Link

https://www.jstage.jst.go.jp/article/cbij/24/0/24_13/_pdf

Reference16 articles.

1. [1] Kim, Y.; Liu, H.; Galasiti, Kankanamalage, A.C.; Weerasekara, S.; Hua, D.H.; et al. Reversal of the progression of fatal coronavirus infection in cats by a broad-spectrum coronavirus protease inhibitor, PLoS Pathog. 2016, 12, e1005531. doi: 10.1371/journal.ppat.1005531.

2. [2] Kim, Y.; Lovell, S.; Tiew. K.C.; Mandadapu, S.R.; Alliston, K.R.; et al. Broad-spectrum antivirals against 3C or 3C-like proteases of picornaviruses, noroviruses, and coronaviruses, J. Virol. 2012, 86, 11754–11762. doi: 10.1128/JVI.01348-12.

3. [3] Kitaura, K.; Ikeo, E.; Asada, T.; Nakano, T.; Uebayasi, M. Fragment Molecular Orbital Method: an Approximate Computational Method for Large Molecules, Chem. Phys. Lett. 1999, 313, 701–706. doi: 10.1016/S0009-2614(99)00874-X

4. [4] Wang, Y.C.; Yang, W.H.; Yang, C.S.; Hou, M.H.; Tsai, C.L.; et al. Structural basis of SARSCoV-2 main protease inhibition by a broad-spectrum anti-coronaviral drug, Am J Cancer Res. 2020, 10, 2535–2545.

5. [5] Watanabe, C.; Watanabe, H.; Okiyama, Y.; Takaya, D.; Fukuzawa, K.; et al. Development of an automated fragment molecular orbital (FMO) calculation protocol toward construction of quantum mechanical calculation database for large biomolecules, CBIJ. 2019, 19, 5–18. doi: 10.1273/cbij.19.5