TY - JOUR
T1 - Special Features of COVID-19 in the FMODB
T2 - Fragment Molecular Orbital Calculations and Interaction Energy Analysis of SARS-CoV-2-Related Proteins
AU - Fukuzawa, Kaori
AU - Kato, Koichiro
AU - Watanabe, Chiduru
AU - Kawashima, Yusuke
AU - Handa, Yuma
AU - Yamamoto, Ami
AU - Watanabe, Kazuki
AU - Ohyama, Tatsuya
AU - Kamisaka, Kikuko
AU - Takaya, Daisuke
AU - Honma, Teruki
N1 - Funding Information:
The authors thank Prof. Yuji Mochizuki and Dr. Koji Okuwaki of Rikkyo University, Prof. Shigenori Tanaka of Kobe University, Dr. Yuto Komeiji of the National Institute of Advanced Industrial Science and Technology, and Dr. Tatsuya Nakano and Dr. Yoshio Okiyama of the National Institute of Health Sciences (NIHS) for general discussions related to FMO calculations. In particular, Prof. Mochizuki provided us the Oakforest-PACS version of ABINIT-MP and the calculation data of the spike protein trimer. The authors are grateful to Prof. Tatsuya Takagi of the Osaka University for discussing the PPI of S protein, Dr. Kazumi Tsuda and Dr. Shu Koyama of Science & Technology Systems, Inc. for their help in the development of the FMODB, and Dr. Junichi Ishida of Mizuho Research & Technologies, Ltd. for his help in some of the calculations. The authors would like to thank Enago for the English language review. This study was partially supported by the Platform Project for Supporting Drug Discovery and Life Science Research (Basis for Supporting Innovative Drug Discovery and Life Science Research) (BINDS) from the Japan Agency for Medical Research and Development (AMED) (Grant Number JP21am0101113). C.W. acknowledges JST, PRESTO grant (JPMJPR18GD). C.W. and D.T. acknowledge JSPS KAKENHI (Grant Number 18K06619). This research was supported by the RIKEN programs for Drug Discovery and Medical Technology Platforms (DMP) and COVID-19 project. This research was performed under the activities of the FMO drug design consortium (FMODD). The FMO calculations were partially performed using the Oakforest-PACS supercomputer (project ID: hp200101), Fugaku supercomputer (project ID: hp210130), the HOKUSAI supercomputer (RIKEN Advanced Center for Computing and Communications, Saitama, Japan, project ID: Q20306), and the TSUBAME3.0 supercomputer (Tokyo Institute of Technology, Tokyo, Japan). A part of PIEDA calculations was performed with the MIZUHO/BioStation software package (version 4.0).
Publisher Copyright:
© 2021 American Chemical Society.
PY - 2021/9/27
Y1 - 2021/9/27
N2 - 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.
AB - 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.
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U2 - 10.1021/acs.jcim.1c00694
DO - 10.1021/acs.jcim.1c00694
M3 - Article
AN - SCOPUS:85115919393
SN - 0095-2338
VL - 61
SP - 4594
EP - 4612
JO - Journal of Chemical Documentation
JF - Journal of Chemical Documentation
IS - 9
ER -
