Structural Insights into Binding of Remdesivir Triphosphate within the Replication–Transcription Complex of SARS-CoV‑2

Remdesivir is an adenosine analogue that has a cyano
substitution
in the C1′ position of the ribosyl moiety and a modified base
structure to stabilize the linkage of the base to the C1′ atom
with its strong electron-withdrawing cyano group. Within the replication–transcription
complex (RTC) of SARS-CoV-2, the RNA-dependent RNA polymerase nsp12
selects remdesivir monophosphate (RMP) over adenosine monophosphate
(AMP) for nucleotide incorporation but noticeably slows primer extension
after the added RMP of the RNA duplex product is translocated by three
base pairs. Cryo-EM structures have been determined for the RTC with
RMP at the nucleotide-insertion (i) site or at the i + 1, i + 2, or i + 3
sites after product translocation to provide a structural basis for
a delayed-inhibition mechanism by remdesivir. In this study, we applied
molecular dynamics (MD) simulations to extend the resolution of structures
to the measurable maximum that is intrinsically limited by MD properties
of these complexes. Our MD simulations provide (i) a structural basis
for nucleotide selectivity of the incoming substrates of remdesivir
triphosphate over adenosine triphosphate and of ribonucleotide over
deoxyribonucleotide, (ii) new detailed information on hydrogen atoms
involved in H-bonding interactions between the enzyme and remdesivir,
and (iii) direct information on the catalytically active complex that
is not easily captured by experimental methods. Our improved resolution
of interatomic interactions at the nucleotide-binding pocket between
remedesivir and the polymerase could help to design a new class of
anti-SARS-CoV-2 inhibitors.