<p>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.</p>
Intermolecular interaction among Remdesivir, RNA and RNA-dependent RNA polymerase of SARS-CoV-2 analyzed by fragment molecular orbital calculation
