posted on 2024-02-27, 18:55authored byGiada Ciardullo, Angela Parise, Mario Prejanò, Tiziana Marino
The nonstructural protein 12, known as RNA-dependent
RNA polymerase
(RdRp), is essential for both replication and repair of the viral
genome. The RdRp of SARS-CoV-2 has been used as a promising candidate
for drug development since the inception of the COVID-19 spread.
In this work, we performed an in silico investigation
on the insertion of the naturally modified pyrimidine nucleobase ddhCTP
into the SARS-CoV-2 RdRp active site, in a comparative analysis with
the natural one (CTP). The modification in ddhCTP involves the removal
of the 3′-hydroxyl group that prevents the addition of subsequent
nucleotides into the nascent strand, acting as an RNA chain terminator
inhibitor. Quantum mechanical investigations helped to shed light
on the mechanistic source of RdRp activity on the selected nucleobases,
and comprehensive all-atom simulations provided insights about the
structural rearrangements occurring in the active-site region when
inorganic pyrophosphate (PPi) is formed. Subsequently, the intricate
pathways for the release of PPi, the catalytic product of RdRp, were
investigated using Umbrella Sampling simulations. The results are
in line with the available experimental data and contribute to a more
comprehensive point of view on such an important viral enzyme.