PPNDS inhibits murine Norovirus RNA‐dependent RNA‐polymerase mimicking two RNA stacking bases

Abstract

a b s t r a c tNorovirus (NV) is a major cause of gastroenteritis worldwide. Antivirals against such important pathogens are on demand. Among the viral proteins that orchestrate viral replication, RNA-dependent-RNA-polymerase (RdRp) is a promising drug development target. From an in silico-docking search focused on the RdRp active site, we selected the compound PPNDS, which showed low micromolar IC 50 vs. murine NV-RdRp in vitro. We report the crystal structure of the murine NVRdRp/PPNDS complex showing that two molecules of the inhibitor bind in antiparallel stacking interaction, properly oriented to block exit of the newly synthesized RNA. Such inhibitor-binding mode mimics two stacked nucleotide-bases of the RdRp/ssRNA complex.

Current tools for norovirus drug discovery

“…MNV has been used as a model system to study HNV, because MNV is used to infect cells and produce an animal model [34]. Since MNV is closely related to HNV, it is often assumed that active compounds in MNV systems are similarly active against HNVs [35]. Recently however, MNV has been shown be an imperfect model to study HNV due to the differences in the capsids of the viruses.…”

“…A detailed review describing the function of norovirus nonstructural proteins has been reported [12]. Since humans lack RdRp enzymes, these enzymes are considered one of the promising targets for anti-norovirus drug development [35] including norovirus 3CLpro. Protease 3CLpro cleaves the long polypeptide chain that translates from ORF1 of viral RNA into multiple non-structural proteins which serve as important enzymes supporting norovirus life cycle.…”

Structural biology in antiviral drug discovery

“…Finally, structural biology has been essential also for the identification of novel inhibitors of norovirus RNA-dependent RNA-polymerase. A docking-based in silico search method on the polymerase structure using commercially available compounds led to the discovery of suramin and its analogues [62] and of PPNDS [63,64] as novel inhibitors of the norovirus RdRp activity. The resolution of the crystal structure of PPNDS in complex with the enzyme has also indicated the possibility to target a new binding sub-pocket in the thumb domain of the enzyme for the design of new norovirus inhibitors [64].…”

Norovirus Vaccines and Potential Antinorovirus Drugs: Recent Advances and Future Perspectives

“…Effective antiviral drugs are needed to reduce HuNoV replication and transmission, especially in hosts that are incapable of clearing the viral infection. Recent antiviral studies have targeted the viral protease [119,120] or RdRp [121–123] or host proteins essential to the viral life cycle, such as deubiquitinase [124]. …”

“…Novel antivirals targeting the viral RdRp focus primarily on nucleoside analogs, but development efforts have also focused on non-nucleoside analogs [123]. Both strategies have been effective in the inhibition of the viral polymerase [121–123]. Non-nucleoside inhibitors have also been effective against Norwalk virus replicon and MNV in vitro and in vivo [123].…”