Probing remdesivir nucleotide analogue insertion to SARS-CoV-2 RNA dependent RNA polymerase in viral replication

Journal Article · Mon Sep 13 00:00:00 EDT 2021 · Molecular Systems Design & Engineering

DOI:https://doi.org/10.1039/d1me00088h· OSTI ID:1982209

Romero, Moises Ernesto ^[1]; Long, Chunhong ^[2]; La Rocco, Daniel ^[3]; Keerthi, Anusha Mysore ^[4]; Xu, Dajun ^[1]; Yu, Jin  ^[1]

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1. University of California, Irvine, CA (United States)
2. Chongqing University of Posts and Telecommunications, Chongqing (China)
3. University of California, Berkeley, CA (United States
4. R.V. College of Engineering, Bengaluru (India)

Remdesivir (RDV) prodrug can be metabolized into a triphosphate form nucleotide analogue (RDV-TP) to bind and insert into the active site of viral RNA dependent RNA polymerase (RdRp) to further interfere with viral genome replication. Here in this work, we computationally studied how RDV-TP binds and inserts to the SARS-CoV-2 RdRp active site, in comparison with natural nucleotide substrate adenosine triphosphate (ATP). To do that, we first constructed atomic structural models of an initial binding complex (active site open) and a substrate insertion complex (active site closed), based on high-resolution cryo-EM structures determined recently for SARS-CoV-2 RdRp or non-structural protein (nsp) 12, in complex with accessory protein factors nsp7 and nsp8. By conducting all-atom molecular dynamics simulation with umbrella sampling strategies on the nucleotide insertion between the open and closed state RdRp complexes, our studies show that RDV-TP can initially bind in a comparatively stabilized state to the viral RdRp active site, as it primarily forms base stacking with the template uracil nucleotide (nt +1), which under freely fluctuations supports a low free energy barrier of the RDV-TP insertion (~1.5 kcal mol^-1). In comparison, the corresponding natural substrate ATP binds initially to the RdRp active site in Watson–Crick base pairing with the template nt, and inserts into the active site with a medium low free energy barrier (~2.6 kcal mol^-1), when the fluctuations of the template nt are well quenched. The simulations also show that the initial base stacking of RDV-TP with the template can be specifically stabilized by motif C-S759, S682 (near motif B) with the base, and motif G-K500 with the template backbone. Although the RDV-TP insertion can be hindered by motif F-R555/R553 interaction with the triphosphate, the ATP insertion seems to be facilitated by such interactions. The inserted RDV-TP and ATP can be further distinguished by specific sugar interaction with motif B-T687 and motif A-D623, respectively.

• Research Organization: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States). Oak Ridge Leadership Computing Facility (OLCF); Univ. of California, Irvine, CA (United States)
• Sponsoring Organization: USDOE Office of Science (SC); National Science Foundation (NSF); Simons Foundation; National Natural Science Foundation of China (NSFC); Natural Science Foundation of Chongqing; Chongqing University of Posts and Telecommunication
• Grant/Contract Number: AC05-00OR22725; 2028935; DMS-1763272; 594598; 12005029; cstc2020jcyjmsxmX0811; A2020-029
• OSTI ID: 1982209
• Journal Information: Molecular Systems Design & Engineering, Vol. 6, Issue 11; ISSN 2058-9689
• Publisher: Royal Society of Chemistry
• Country of Publication: United States
• Language: English

Related Subjects

36 MATERIALS SCIENCE
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
42 ENGINEERING