The structural model of Zika virus RNA-dependent RNA polymerase in complex with RNA for rational design of novel nucleotide inhibitors

Jakub Šebera,Vladimír Sychrovský,Anna Dubankova,Daniel Ruzek,Evzen Boura,Radim Nencka

doi:10.1038/s41598-018-29459-7

Abstract

Zika virus is a global health threat due to significantly elevated risk of fetus malformations in infected pregnant women. Currently, neither an effective therapy nor a prophylactic vaccination is available for clinical use, desperately necessitating novel therapeutics and approaches to obtain them. Here, we present a structural model of the Zika virus RNA-dependent RNA polymerase (ZIKV RdRp) in complex with template and nascent RNAs, Mg2+ ions and accessing nucleoside triphosphate. The model allowed for docking studies aimed at effective pre-screening of potential inhibitors of ZIKV RdRp. Applicability of the structural model for docking studies was illustrated with the NITD008 artificial nucleotide that is known to effectively inhibit the function of the ZIKV RdRp. The ZIKV RdRp – RNA structural model is provided for all possible variations of the nascent RNA bases pairs to enhance its general utility in docking and modelling experiments. The developed model makes the rational design of novel nucleosides and nucleotide analogues feasible and thus provides a solid platform for the development of advanced antiviral therapy.

Highlights

Zika virus (ZIKV) is an emerging mosquito-borne member of the family Flaviviridae, genus Flavivirus
For these reasons we endeavoured to build a sophisticated model of RNA and nucleotide bound ZIKV RNA-dependent RNA polymerase (RdRp) based on the published crystal structures of ZIKV RdRp and its most similar RdRp bound to RNA that can be found in the PDB database which is the Hepatitis C virus (HCV) RdRp
The ZIKV RdRp:RNA model employed in hybrid quantum mechanics/molecular mechanics (QM/MM) calculations was derived from the ZIKV RdRp (PDB ID 5TFR) and HCV (PDB ID 4WTD) crystal structures because no flaviviral RdRp was so far crystallized in complex with RNA

Summary

Introduction

Zika virus (ZIKV) is an emerging mosquito-borne member of the family Flaviviridae, genus Flavivirus. Several crystal structures of other flavivirus polymerases were solved in complex with small molecules[25,26], neither of these structures contained an RNA molecule nor any nucleotide or nucleotide analog, which hinders their use in structure based design of novel inhibitors For these reasons we endeavoured to build a sophisticated model of RNA and nucleotide bound ZIKV RdRp based on the published crystal structures of ZIKV RdRp and its most similar RdRp bound to RNA that can be found in the PDB database which is the Hepatitis C virus (HCV) RdRp. For these reasons we endeavoured to build a sophisticated model of RNA and nucleotide bound ZIKV RdRp based on the published crystal structures of ZIKV RdRp and its most similar RdRp bound to RNA that can be found in the PDB database which is the Hepatitis C virus (HCV) RdRp Such a functional model of ZIKV RdRp containing all the necessary components is indispensable for successful docking experiments, which are an essential part of the rational design of inhibitors that might serve as drugs against ZIKV and other flaviviruses. Correctness of the ZIKV RdRp:RNA structural model developed in this work is demonstrated biochemically using point mutants predicted from the structural model and the usefulness of our model is documented using docking experiments

Methods

Results

Discussion

Conclusion