Flaviviridae viruses use a common molecular mechanism to escape nucleoside analogue inhibitors.
The RNA-dependent RNA polymerases of Flaviviridae viruses are crucial for replication. The Flaviviridae polymerase is organized into structural motifs (A-G), with motifs F, A, C and E containing interrogating, priming and catalytic substrate-interacting sites. Modified nucleoside analogues act as antiviral drugs by targeting Flaviviridae polymerases and integrating into the synthesized product causing premature termination. A threonine mutation of a conserved serine residue in motif B of Flaviviridae polymerases renders resistance to 2'-C-methylated nucleoside analogues. The mechanism how this single mutation causes Flaviviridae viruses to escape nucleoside analogues is not yet known. Given the pivotal position of the serine residue in motif B that supports motif F, we hypothesized the threonine mutation causes alterations in nucleoside exploration within the entry tunnel. Implementing a stochastic molecular software showed the all-atom 2'-C-methylated analogue reaction within the active sites of wild type and serine-threonine mutant polymerases from Hepacivirus and Flavivirus. Compared with the wild type, the serine-threonine mutant polymerases caused a significant decrease of analogue contacts with conserved interrogating residues in motif F and a displacement of metal ion cofactors. The simulations significantly showed that during the analogue exploration of the active site the hydrophobic methyl group in the serine-threonine mutant repels water-mediated hydrogen bonds with the 2'-C-methylated analogue, causing a concentration of water-mediated bonds at the substrate-interacting sites. Collectively, the data are an insight into a molecular escape mechanism by Flaviviridae viruses from 2'-C-methylated nucleoside analogue inhibitors.
Institute of Parasitology, The Czech Academy of Sciences, Branišovská 31, CZ-37005 České Budějovice, Czechia; Department of Virology, Veterinary Research Institute, Hudcova 70, CZ-62100 Brno, Czechia. Electronic address: valdjj@gmail.com.
James J
JJ
Valdés
Biology Center, Czech Academy of Sciences, University of South Bohemia, Branišovská 31, CZ-37005 České Budějovice, Czechia.
Philip T
PT
Butterill
Institute of Parasitology, The Czech Academy of Sciences, Branišovská 31, CZ-37005 České Budějovice, Czechia; Department of Virology, Veterinary Research Institute, Hudcova 70, CZ-62100 Brno, Czechia.
Daniel
D
Růžek
D001665:Binding Sites; D004789:Enzyme Activation; D004791:Enzyme Inhibitors / Q000737:chemistry*; D018067:Flaviviridae / Q000737:chemistry* / Q000201:enzymology*; D009705:Nucleosides / Q000737:chemistry*; D011485:Protein Binding; D012324:RNA-Dependent RNA Polymerase / Q000737:chemistry*
D004791:Enzyme Inhibitors; D009705:Nucleosides; D012324:RNA-Dependent RNA Polymerase
Analogue; Flaviviridae; Interrogating; Polymerase; Virus; Water