Abstract
The flavivirus family contains several important human pathogens, such as Zika virus (ZIKV), dengue, West Nile, and Yellow Fever viruses, that collectively lead to a large, global disease burden. Currently, there are no approved medicines that can target these viruses. The sudden outbreak of ZIKV infections in 2015–2016 posed a serious threat to global public health. While the epidemic has receded, persistent reservoirs of ZIKV infection can cause reemergence. Here, we have used X-ray crystallography-based screening to discover two novel sites on ZIKV NS3 helicase that can bind drug-like fragments. Both sites are structurally conserved in other flaviviruses, and mechanistically significant. The binding poses of four fragments, two for each of the binding sites, were characterized at atomic precision. Site A is a surface pocket on the NS3 helicase that is vital to its interaction with NS5 polymerase and formation of the flaviviral replication complex. Site B corresponds to a flexible, yet highly conserved, allosteric site at the intersection of the three NS3 helicase domains. Saturation transfer difference nuclear magnetic resonance (NMR) experiments were additionally used to evaluate the binding strength of the fragments, revealing dissociation constants (KD) in the lower mM range. We conclude that the NS3 helicase of flaviviruses is a viable drug target. The data obtained open opportunities towards structure-based design of first-in-class anti-ZIKV compounds, as well as pan-flaviviral therapeutics.
Highlights
The recent outbreak of Zika virus (ZIKV), a mosquito-borne flavivirus, in the Americas and the Pacific, triggered a public health crisis, leading the World Health Organization to declare ZIKV infections as a global emergency [1]
To conduct an fragment-based screening (FBS)-X study, it was imperative to develop an efficient protocol towards Escherichia coli overexpression and purification of ZIKV NS3-Hel
After several rounds of optimization, single 3D crystals that diffracted X-rays to beyond 2.5 Å resolution could be reproducibly obtained, which was a prerequisite for subsequent fragment-based screening by X-ray crystallography (FBS-X) experiments
Summary
The recent outbreak of Zika virus (ZIKV), a mosquito-borne flavivirus, in the Americas and the Pacific, triggered a public health crisis, leading the World Health Organization to declare ZIKV infections as a global emergency [1]. Over 1.67 M cases were reported in Brazil [2], with another 41,957 cases in the United States and its territories [3]. This wave of ZIKV infections resulted in a sudden rise in neurological complications, the most severe of which are microcephaly or congenital fetal malformation in children born to infected women [4], and Guillain–Barre syndrome [5].
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