Structure-based discovery of antiviral inhibitors targeting the E dimer interface of Japanese encephalitis virus

https://doi.org/10.1016/j.bbrc.2019.05.148Get rights and content

Highlights

  • The fusion-loop pocket of flavivirus could be one conserved and promising target for the blockage of E dimer interaction.

  • Virtual screening followed by docking has been one of the reputable methods for drug discovery.

  • ChemDiv-3 could impair the formation of JEV sE dimer.

Abstract

Flaviviruses are emerging arthropod-borne viruses posing a great threat to human beings worldwide. The E dimer configuration of the flavivirus was prominent during viral assembly, maturation and entry. Neutralization antibodies targeting E dimer played the important role in controlling the flavivirus infection. Previously, the ideal drug target of small molecular inhibitors of JEV was viral proteases and polymerases. The crystal structure of JEV E protein showed a conserved pocket in it is important at membrane fusion step. Recently, a set of anti-virus drugs has been found by virtual screening. Here, we show that the fusion-loop pocket of JEV E protein was a conservative region and an ideal drug target. ChemDiv-3 from virtual screening as the lead compound was found to show a relatively modest inhibition effect for JEV in vitro and in vivo test and could interfere with the formation of JEV sE dimer. ChemDiv-3 interacts with the amino acid residues ASN 313, PRO 314, ALA 315, and VAL 323 in E protein via hydrogen bonds for occupation of the fusion-loop pocket. The key binding sites LYS 312, ALA 513 and THR 317 forming the fusion-loop pocket are the same and other auxiliary sites are similar among the flavivirus. Taken together, the fusion-loop pocket of the flavivirus could be one promising target for drug discovery.

Introduction

Japanese encephalitis virus (JEV) is a member of the genus flavivirus and family Flaviviridae, which include yellow fever virus, West Nile virus, Dengue virus and Zika virus. JEV is the main cause of viral encephalitis worldwide, risking over 3 billion people in East and Southeast Asia and northern Australia [1]. JEV causes a range of severe central nervous system disorders and neurologic sequelae including persistent motor defects and cognitive and language impairments [2]. However, beyond intensive supportive care, no specific and effective therapies are expected to be available.

JEV is a positive-stranded RNA virus with an approximately 11-kb genome that is translated as a single polyprotein that is cleaved by host and viral proteases into structural capsid (C), premembrane (prM), and envelope (E) proteins and seven nonstructural proteins [3]. Recently, many compounds have been shown to be effective inhibitors against several flavivirus by targeting their non-structural (NS) proteins, such as NS2B-NS3, NS3 helicase, NS4B, NS5 methyltransferase, and NS5 RNA-dependent RNA polymerase (RdRp) [[4], [5], [6], [7], [8]].

On the surface of the mature virion, flavivirus E proteins exist as an antiparallel dimer with the fusion peptide of DII nestled into a cavity constituted by DI and DIII on the opposing subunit with functional importance in the virus life cycle [9]. Different from other flavivirus, the JEV dimer is maintained mainly by fusion loop-fusion loop pocket interaction, deficient of DII-DII contacts. And, we recently demonstrated the structure of JEV-specific monoclonal antibodies 2F2 and 2H4, which revealed the atomic details of antibodies binding and point to quaternary epitopes that span across three functionally important domains from three adjacent envelope proteins [10]. In addition, Priscilla L. Yang has reported small molecules could inhibit dengue virus fusion by binding to a specific pocket on E [11]. Therefore, development of antiviral molecules to impede the function of E dimer could be one effective drugs design strategies.

Virtual screening is widely used in drug discovery to search libraries of small molecules binding to a drug target, typically a protein receptor or enzyme [12]. Numerous tools are designed for these computational analyses, categorized as being ligand-based and receptor-based. Ligand based strategy is designed to find lead compounds with similar pharmacophore elements derived from a specific functional ligand family to find similar [13]. Receptor-based strategy is based on docking of candidate compounds to target pocket or interface with proven or simulated structures [14]. Recently, a set of anti-virus drugs has been found by virtual screening and shown great inhibition activity.

In this study, the fusion loop pocket of JEV based drug design was utilized to screen lead compounds from Chemdiv database for targeting the formation of E dimer. The hitting lead compound has shown antiviral activity in vitro and vivo, which offers one new potential therapeutic target for the treatment of JEV infection.

Section snippets

Pharmacophore modelling and virtual screening

The three-dimensional structure of JEV E protein was obtained from the Protein Data Bank (PDB code 5YWP). The structure is a complex of one anti-JEV E mab 2F2 and E dimer. Prior to molecular modelling and docking, the protein structure was prepared using the Chimera software. One E dimer was kept and the interaction between fusion loop and fusion loop pocket was analyzed. The side chains of W101 and F108 of E were used for pharmacophore modelling by Ligandscout v3.10. Created pharmacophore

Pharmacophore virtual screening targeting of fusion-loop pocket of JEV E

On the surface of the mature virion, JEVE proteins exist as an antiparallel dimer with the fusion peptide of DII nestled into a cavity formed by DI and DIII on the opposing subunit. A set of residues (residues W101 and F108) were critical for fusion-loop functionality, either directly mediating membrane fusion or stabilizing the position of JEV E dimer. The pharmacophore model was produced based on the structure of residues W101 and F108 followed by virtual screening of the ChemDiv database.

Discussion

Given the potential severity of Japanese encephalitis, and its ability to emerge in previously nonendemic areas, the lack of specific treatment for Japanese encephalitis received great attention. Direct-acting antiviral drugs by targeting NS3 and NS2-NS3 interaction have been reported recently and could be promising candidates for JEV treatment. Recently, the importance of flavivirus E protein in viral entry and fusion suggests that it is an effective drug target. Melissanne revealed that

Potential conflicts of interest

All authors: No reported conflicts.

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    These authors contributed equally to this work.

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