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Technical Data of In Silico Analysis of the Interaction of Dietary Flavonoid Compounds against Spike-Glycoprotein and Proteases of SARS-CoV-2

Author

Listed:
  • Nurbella Sofiana Altu

    (Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia)

  • Cahyo Budiman

    (Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia)

  • Rafida Razali

    (Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia)

  • Ruzaidi Azli Mohd Mokhtar

    (Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia)

  • Khairul Azfar Kamaruzaman

    (Biotechnology Research Institute, Universiti Malaysia Sabah, Kota Kinabalu 88400, Sabah, Malaysia)

Abstract

The spike glycoprotein (S protein), 3-chymotrypsin-like protease (3CL-Pro), and papain-like protease (PL-Pro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus are widely targeted for the discovery of therapeutic compounds against this virus. Dietary flavonoid compounds were proposed as a candidate for safe therapy for COVID-19 patients. Nevertheless, wet lab experiments for high-throughput screening of the compounds are undoubtedly time and cost consuming. This study aims to screen dietary flavonoid compounds that bind to S protein, 3CL-Pro, and PL-Pro of SARS-CoV-2. For this purpose, protein structures of the receptor-binding domain (RBD) of S protein (6M0J), 3CL-Pro (6LU7), and PL-Pro (6W9C) were retrieved from the RCSB Protein Data Bank (PDB). Twelve dietary flavonoid compounds were selected for the studies on their binding affinity to the targeted proteins by global and local docking. The docking and molecular dynamic (MD) simulations were performed using YASARA software. Out of 12 compounds, the highest binding score was observed between hesperidin against RBD S protein (−9.98 kcal/mol), 3CL-Pro (−9.43 kcal/mol), and PL-Pro (−8.89 kcal/mol) in global docking. Interestingly, MD simulation revealed that the complex between 3CL-Pro and RBD S protein has better stability than PL-Pro. This study suggests that hesperidin might have versatile inhibitory properties against several essential proteins of SARS-CoV-2. This study, nevertheless, remains to be confirmed through in vitro and in vivo assays.

Suggested Citation

  • Nurbella Sofiana Altu & Cahyo Budiman & Rafida Razali & Ruzaidi Azli Mohd Mokhtar & Khairul Azfar Kamaruzaman, 2022. "Technical Data of In Silico Analysis of the Interaction of Dietary Flavonoid Compounds against Spike-Glycoprotein and Proteases of SARS-CoV-2," Data, MDPI, vol. 7(11), pages 1-24, October.
    • Handle: RePEc:gam:jdataj:v:7:y:2022:i:11:p:144-:d:955395
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    References listed on IDEAS

    as
    1. Rafida Razali & Vijay Kumar Subbiah & Cahyo Budiman, 2021. "Technical Data of Heterologous Expression and Purification of SARS-CoV-2 Proteases Using Escherichia coli System," Data, MDPI, vol. 6(9), pages 1-13, September.
    2. Jerzy Osipiuk & Saara-Anne Azizi & Steve Dvorkin & Michael Endres & Robert Jedrzejczak & Krysten A. Jones & Soowon Kang & Rahul S. Kathayat & Youngchang Kim & Vladislav G. Lisnyak & Samantha L. Maki &, 2021. "Structure of papain-like protease from SARS-CoV-2 and its complexes with non-covalent inhibitors," Nature Communications, Nature, vol. 12(1), pages 1-9, December.
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