Special Features of COVID-19 in the FMODB: Fragment Molecular Orbital Calculations and Interaction Energy Analysis of SARS-CoV-2-Related Proteins

被引：16

作者：

Fukuzawa, Kaori ^{[1
,6
]}

Kato, Koichiro ^{[7
,8
]}

Watanabe, Chiduru ^{[4
,9
]}

Kawashima, Yusuke ^{[1
]}

Handa, Yuma ^{[1
]}

Yamamoto, Ami ^{[1
]}

Watanabe, Kazuki ^{[2
,3
]}

Ohyama, Tatsuya ^{[4
,5
]}

Kamisaka, Kikuko ^{[4
]}

Takaya, Daisuke ^{[4
]}

Honma, Teruki ^{[4
]}

机构：

[1] Hoshi Univ, Sch Pharm & Pharmaceut Sci, Dept Phys Chem, Tokyo 1428501, Japan

[2] Osaka Univ, Grad Sch Pharmaceut Sci, Suita, Osaka 5650871, Japan

[3] Chiba Univ, Grad Sch Pharmaceut Sci, Chiba 2608675, Japan

[4] RIKEN Ctr Biosyst Dynam Res, Yokohama, Kanagawa 2300045, Japan

[5] Konan Univ, Frontier Inst Biomol Engn Res FIBER, Kobe, Hyogo 6500047, Japan

[6] Tohoku Univ, Dept Biomol Engn, Grad Sch Engn, Sendai, Miyagi 9808579, Japan

[7] Kyushu Univ, Dept Appl Chem, Grad Sch Engn, Fukuoka 8190395, Japan

[8] Kyushu Univ, Ctr Mol Syst CMS, Fukuoka 8190395, Japan

[9] JST PRESTO, Kawaguchi, Saitama 3320012, Japan

来源：

JOURNAL OF CHEMICAL INFORMATION AND MODELING | 2021年 / 61卷 / 09期

关键词：

DOMAIN; PROTEASE; IDENTIFICATION; REPLICATION; DYNAMICS; DATABASE; TOOLS;

D O I：

10.1021/acs.jcim.1c00694

中图分类号：

R914 [药物化学];

学科分类号：

100701 ;

摘要：

SARS-CoV-2 is the causative agent of coronavirus (known as COVID-19), the virus causing the current pandemic. There are ongoing research studies to develop effective therapeutics and vaccines against COVID-19 using various methods and many results have been published. The structure-based drug design of SARS-CoV-2-related proteins is promising, however, reliable information regarding the structural and intra-and intermolecular interactions is required. We have conducted studies based on the fragment molecular orbital (FMO) method for calculating the electronic structures of protein complexes and analyzing their quantitative molecular interactions. This enables us to extensively analyze the molecular interactions in residues or functional group units acting inside the protein complexes. Such precise interaction data are available in the FMO database (FMODB) (fittps://drugdesign.riken.jp/FMODB/). Since April 2020, we have performed several FMO calculations on the structures of SARS-CoV-2-related proteins registered in the Protein Data Bank. We have published the results of 681 structures, including three structural proteins and 11 nonstructural proteins, on the COVID-19 special page (as of June 8, 2021). In this paper, we describe the entire COVID-19 special page of the FMODB and discuss the calculation results for various proteins. These data not only aid the interpretation of experimentally determined structures but also the understanding of protein functions, which is useful for rational drug design for COVID-19.

引用

页码：4594 / 4612

页数：19

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