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

Kaori Fukuzawa, Koichiro Kato, Chiduru Watanabe, Yusuke Kawashima, Yuma Handa, Ami Yamamoto, Kazuki Watanabe, Tatsuya Ohyama, Kikuko Kamisaka, Daisuke Takaya, Teruki Honma

    Research output: Contribution to journalArticlepeer-review

    Abstract

    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) (https://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.

    Original languageEnglish
    JournalJournal of Chemical Information and Modeling
    DOIs
    Publication statusAccepted/In press - 2021

    All Science Journal Classification (ASJC) codes

    • Chemistry(all)
    • Chemical Engineering(all)
    • Computer Science Applications
    • Library and Information Sciences

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