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Intermolecular interaction among Remdesivir, RNA and RNA-dependent RNA polymerase of SARS-CoV-2 analyzed by fragment molecular orbital calculation.
Kato, Koichiro; Honma, Teruki; Fukuzawa, Kaori.
  • Kato K; Department of Applied Chemistry, Graduate School of Engineering, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan; Center for Molecular Systems (CMS), Kyushu University, 744 Motooka, Nishi-ku, Fukuoka, 819-0395, Japan. Electronic address: kato.koichiro.957@m.kyushu-u.ac.jp.
  • Honma T; RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan. Electronic address: honma.teruki@riken.jp.
  • Fukuzawa K; Department of Physical Chemistry, 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. Electronic address: k-fukuzawa@hoshi.ac.jp.
J Mol Graph Model ; 100: 107695, 2020 11.
Article in English | MEDLINE | ID: covidwho-652785
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ABSTRACT
COVID-19, a disease caused by a new strain of coronavirus (SARS-CoV-2) originating from Wuhan, China, has now spread around the world, triggering a global pandemic, leaving the public eagerly awaiting the development of a specific medicine and vaccine. In response, aggressive efforts are underway around the world to overcome COVID-19. In this study, referencing the data published on the Protein Data Bank (PDB ID 7BV2) on April 22, we conducted a detailed analysis of the interaction between the complex structures of the RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 and Remdesivir, an antiviral drug, from the quantum chemical perspective based on the fragment molecular orbital (FMO) method. In addition to the hydrogen bonding and intra-strand stacking between complementary strands as seen in normal base pairs, Remdesivir bound to the terminus of an primer-RNA strand was further stabilized by diagonal π-π stacking with the -1A' base of the complementary strand and an additional hydrogen bond with an intra-strand base, due to the effect of chemically modified functional group. Moreover, stable OH/π interaction is also formed with Thr687 of the RdRp. We quantitatively revealed the exhaustive interaction within the complex among Remdesivir, template-primer-RNA, RdRp and co-factors, and published the results in the FMODB database.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Antiviral Agents / Viral Proteins / RNA-Dependent RNA Polymerase / RNA, Viral / Adenosine Monophosphate / Alanine / Betacoronavirus Topics: Vaccines Language: English Journal: J Mol Graph Model Journal subject: Molecular Biology Year: 2020 Document Type: Article

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Antiviral Agents / Viral Proteins / RNA-Dependent RNA Polymerase / RNA, Viral / Adenosine Monophosphate / Alanine / Betacoronavirus Topics: Vaccines Language: English Journal: J Mol Graph Model Journal subject: Molecular Biology Year: 2020 Document Type: Article