Structural Insight into NS5 of Zika Virus Leading to the Discovery of MTase Inhibitors

Abstract

Zika virus (ZIKV) is an emerging mosquito-borne virus recently linked to intrauterine growth restriction including abnormal fetal brain development. The recent outbreak of ZIKV reached pandemic level resulting in an alarming public health emergency. At present, there is limited understanding of the infectious mechanism and no approved therapy. Nonstructural protein 5 is essential for capping and replication of viral RNA and comprises a methyltransferase (MTase) and RNA dependent RNA polymerase domain. Here we used molecular modeling to obtain the structure of ZIKV MTase and molecular docking to identify the additional hydrophobic region uniquely conserved in flavivirus MTase that can be used as a druggable site. Subsequently, a virtual screening with a library of 28 341 compounds identified 10 best hits showing decisive contacts with the MTase. In vitro efficacy analysis of these compounds against ZIKV, by plaque reduction assay, has confirmed four of the top scored ligands (Life Chemicals ID: F3043-0013, F0922-0796, F1609-0442, and F1750-0048) having EC50 (50% effective concentration) values of 4.8 ± 2.3, 12.5 ± 7.4, 17.5 ± 8.4, and 17.6 ± 3.1 μM respectively, identifying lead compounds for anti-ZIKV drug development.

The A–Z of Zika drug discovery

“…The structure of ZIKV MTase with the SAM analog sinefungin was recently elucidated, and the construction of an inhibitor connecting sinefungin with a Cap analog attached by a linker was proposed, which could perhaps grant higher affinity to the protein [91]. VS using a hydrophobic site close to the SAM pocket was performed with >20 000 compounds [92]. The ten compounds with the best scores were selected for experimental screening: four were able to inhibit viral growth in concentrations below 20 mM and the best inhibitor presented an IC 50 value of 4.8 mM [92].…”

The Race To Find Antivirals for Zika Virus

“…The NS5 protein of ZIKV exhibits not only RdRp activity, but also displays a methyltransferase domain responsible for capping the 5= end of viral genomic RNA. This enzymatic activity has just started to be explored as a potential antiviral target to combat ZIKV (27)(28)(29). ZIKV proteins other than NS5 also constitute potential druggable antiviral targets.…”

Zika Virus: What Have We Learnt Since the Start of the Recent Epidemic?

“…NS5 is the viral RNA-dependent RNA polymerase that is in charge of genome replication constituting a major target for antiviral design (Lu et al, 2017;Xu et al, 2017). Furthermore, the analysis of the structure of the methyltransferase domain of NS5, which is responsible for capping the 5 end of the viral genomic RNA, also provides new opportunities for the design of antiviral compounds (Coloma et al, 2016;Stephen et al, 2016;Coutard et al, 2017;Zhou et al, 2017). Besides its function in genome replication and capping, NS5 from ZIKV also contributes to viral multiplication by inhibiting interferon signaling (Grant et al, 2016).…”