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Intermolecular Interaction Analyses on SARS-CoV-2 Spike Protein Receptor Binding Domain and Human Angiotensin-Converting Enzyme 2 Receptor-Blocking Antibody/Peptide Using Fragment Molecular Orbital Calculation

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Download Hi-Res ImageDownload to MS-PowerPointCite This:J. Phys. Chem. Lett. 2021, 12, 16, 4059-4066
    Physical Insights into Quantum Phenomena and Function

    Intermolecular Interaction Analyses on SARS-CoV-2 Spike Protein Receptor Binding Domain and Human Angiotensin-Converting Enzyme 2 Receptor-Blocking Antibody/Peptide Using Fragment Molecular Orbital Calculation
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    • Kazuki Watanabe
      Kazuki Watanabe
      Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
      More by Kazuki Watanabe
    • Chiduru Watanabe*
      Chiduru Watanabe
      Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
      JST PRESTO, 4-1-8, Honcho, Kawaguchi, Saitama 332-0012, Japan
      *Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan. Email: [email protected]
      More by Chiduru Watanabe
      Orcidhttp://orcid.org/0000-0002-0742-3896
    • Teruki Honma
      Teruki Honma
      Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
      More by Teruki Honma
      Orcidhttp://orcid.org/0000-0003-3761-9504
    • Yu-Shi Tian
      Yu-Shi Tian
      Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
      More by Yu-Shi Tian
    • Yusuke Kawashima
      Yusuke Kawashima
      School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
      More by Yusuke Kawashima
    • Norihito Kawashita
      Norihito Kawashita
      Graduate School of Science and Engineering Research, Kindai University, 3-4-1 Kowakae, Higashiosaka, Osaka 577-8502, Japan
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      Orcidhttp://orcid.org/0000-0002-1740-7232
    • Tatsuya Takagi*
      Tatsuya Takagi
      Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871, Japan
      *Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita City, Osaka 565-0871, Japan. Email: [email protected]
      More by Tatsuya Takagi
    • Kaori Fukuzawa*
      Kaori Fukuzawa
      School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan
      Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, 6-6-11 Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan
      *School of Pharmacy and Pharmaceutical Sciences, Hoshi University, 2-4-41 Ebara, Shinagawa-ku, Tokyo 142-8501, Japan. Email: [email protected]
      More by Kaori Fukuzawa
      Orcidhttp://orcid.org/0000-0001-5357-8250
    Other Access OptionsSupporting Information (1)

    The Journal of Physical Chemistry Letters

    Cite this: J. Phys. Chem. Lett. 2021, 12, 16, 4059–4066
    Click to copy citationCitation copied!
    https://doi.org/10.1021/acs.jpclett.1c00663
    Published April 21, 2021
    Copyright © 2021 American Chemical Society
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    Abstract

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    The spike glycoprotein (S-protein) mediates SARS-CoV-2 entry via intermolecular interaction with human angiotensin-converting enzyme 2. The receptor binding domain (RBD) of the S-protein has been considered critical for this interaction and acts as the target of numerous neutralizing antibodies and antiviral peptides. This study used the fragment molecular orbital method to analyze the interactions between the RBD and antibodies/peptides and extracted crucial residues that can be used as epitopes. The interactions evaluated as interfragment interaction energy values between the RBD and 12 antibodies/peptides showed a fairly good correlation with the experimental activity pIC50 (R2 = 0.540). Nine residues (T415, K417, Y421, F456, A475, F486, N487, N501, and Y505) were confirmed as being crucial. Pair interaction energy decomposition analyses showed that hydrogen bonds, electrostatic interactions, and π-orbital interactions are important. Our results provide essential information for understanding SARS-CoV-2–antibody/peptide binding and may play roles in future antibody/antiviral drug design.

    Copyright © 2021 American Chemical Society

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    Supporting Information

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    The Supporting Information is available free of charge at https://pubs.acs.org/doi/10.1021/acs.jpclett.1c00663.

    • Example of a computational model (PDB entry 6XCM) (Figure S1) (only the monomeric RBD-antibody/peptide was preserved for the FMO calculation), structural information about each calculation model and interaction energies for RBD-antibody/peptide interactions (Table S1), IFIE-sum of region 1 (R403–Y421), region 2 (RBM), and All (RBD) and the ratio of the IFIE-sum of region 1 or region 2 to the total IFIE-sum (Table S2), relationship between residues on the RBD and the number of structures identified as important residues (Table S3), PIEDA results of antibody/peptide residues on the RBD [only region 1 (Seq# 403–421) and region 2 (RBM)] (Table S4), interaction energies among the nine key residues on the RBD and antibodies/peptides (Table S5), XH–Y hydrogen bonds between nine key residues on the SARS-CoV-2 RBD and BD-629 Fab (Table S6), and XH/π interactions between nine key residues with the SARS-CoV-2 RBD and BD-629 Fab (Table S7) (PDF)

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    Cited By

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    This article is cited by 18 publications.

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    The Journal of Physical Chemistry Letters

    Cite this: J. Phys. Chem. Lett. 2021, 12, 16, 4059–4066
    Click to copy citationCitation copied!
    https://doi.org/10.1021/acs.jpclett.1c00663
    Published April 21, 2021
    Copyright © 2021 American Chemical Society
    Request reuse permissions

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