Novel inhibitors targeting Venezuelan equine encephalitis virus capsid protein identified using In Silico Structure-Based-Drug-Design

Sharon Shechter,David A Jans,Chelsea Pinkham,Lindsay Lundberg,Shih-Chao Lin,David R Thomas,Kylie M Wagstaff,Aaron Debono,Kylene Kehn-Hall

doi:10.1038/s41598-017-17672-9

Sharon Shechter, David A Jans + Show 7 more

Open Access

https://doi.org/10.1038/s41598-017-17672-9

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Journal: Scientific Reports	Publication Date: Dec 1, 2017
Citations: 25	License type: open-access

Affiliation: Monash University, George Mason University

Abstract

Therapeutics are currently unavailable for Venezuelan equine encephalitis virus (VEEV), which elicits flu-like symptoms and encephalitis in humans, with an estimated 14% of cases resulting in neurological disease. Here we identify anti-VEEV agents using in silico structure-based-drug-design (SBDD) for the first time, characterising inhibitors that block recognition of VEEV capsid protein (C) by the host importin (IMP) α/β1 nuclear transport proteins. From an initial screen of 1.5 million compounds, followed by in silico refinement and screening for biological activity in vitro, we identified 21 hit compounds which inhibited IMPα/β1:C binding with IC50s as low as 5 µM. Four compounds were found to inhibit nuclear import of C in transfected cells, with one able to reduce VEEV replication at µM concentration, concomitant with reduced C nuclear accumulation in infected cells. Further, this compound was inactive against a mutant VEEV that lacks high affinity IMPα/β1:C interaction, supporting the mode of its antiviral action to be through inhibiting C nuclear localization. This successful application of SBDD paves the way for lead optimization for VEEV antivirals, and is an exciting prospect to identify inhibitors for the many other viral pathogens of significance that require IMPα/β1 in their infectious cycle.

Highlights

Therapeutics are currently unavailable for Venezuelan equine encephalitis virus (VEEV), which elicits flu-like symptoms and encephalitis in humans, with an estimated 14% of cases resulting in neurological disease
The fact that 1111684 shows robust anti-VEEV activity comparable to that of Ivermectin makes it an interesting prospect for further development. This is the first study to use the solved structure of IMPα bound to VEEV-C nuclear localization signal (NLS) as the basis for SBDD to identify small molecule inhibitors of the IMPα:C interaction
A key to our approach was to define and use the minimal/ core NLS of C to delineate the C NLS binding pocket on IMPα, which we investigated in more detail using in silico alanine mutagenesis/docking analysis to identify the likely key residues of IMPα involved in binding

Summary

Introduction

Therapeutics are currently unavailable for Venezuelan equine encephalitis virus (VEEV), which elicits flu-like symptoms and encephalitis in humans, with an estimated 14% of cases resulting in neurological disease. VEEV C is believed to bind to IMPα, as well as to the host nuclear export protein exportin 1, leading to inhibition of host cell nuclear trafficking through either IMP/exportin 1 sequestration and/or blocking of the NPC itself[19], thereby impacting host cell stress/innate immune responses[10]. This function of C has been mapped to amino acids (aa) 33-68, which contain an IMPα/β1-recognised NLS

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