Exploiting host kinases to combat dengue virus infection and disease

Abstract

The burden of dengue on human health has dramatically increased in recent years, underscoring the urgent need for effective therapeutic interventions. Despite decades of research since the discovery of the dengue virus, no specific antiviral treatments are available and strategies to reliably prevent severe disease remain limited. Direct-acting antivirals against dengue are under active investigation but have shown limited efficacy to date. An underappreciated Achille's heal of the virus is its dependence on host factors for infection and pathogenesis, each of which presents a potential avenue for therapeutic intervention. We and others have demonstrated that dengue virus relies on multiple host kinases, some of which are already targeted by clinically approved inhibitors. These offer drug repurposing opportunities for host-directed dengue treatment. Here, we summarize findings on the role of kinases in dengue infection and disease and highlight potential kinase targets for the development of innovative host-directed therapeutics.

Keywords: Dengue virus; Flavivirus; Host-targeted antivirals; Kinase inhibitors; Kinase signaling; Neglected tropical disease.

Figure 1.

Binning Analysis to Identify Bona fide Kinase regulators of DENV. Kinases which were studied in the context of dengue infection or disease were subjected to a binning analysis. All kinases identified are shown at the top. Kinases which were found to be restriction factors of DENV, kinases with evidence in only a single cell type or a single study, and kinases with inconsistent or null roles were binned out as indicated. Within each bin, kinases were categorized by the type of phenotype that was observed, where kinases which were identified through either a genetic or chemical perturbation are teal, kinase responses which were characterized following infection are orange, and kinases which have evidence of both phenotype settings are purple. Bona fide dengue regulators shown at the bottom are kinases that were not down-selected by any of the criteria we applied.

Figure 2.

Phosphosignaling network of bona fide kinases and their intermediate substrates. Bonafide DENV kinases were input into PhosphoSitePlus^® to identify interactions between each kinase. For indirect interactions, the shortest substrate path was queried. The resulting interactions were visualized using Cytoscape, where each node is a kinase, and each edge is an interaction. The shape at either end of each edge indicates the directionality of the interaction, where a circle represents the source kinase, and an arrow represents the target kinase. Cytoscape’s yFiles hierarchic layout feature was applied to the visualized network to spatially organize nodes such that source nodes are situated at the bottom of the network and target nodes are placed above, then nodes were manually relocated to maximize visualization of interaction directionality. Orange nodes represent bonafide DENV kinases, and blue nodes represent their substrates and regulators. Dark blue node outline indicates the availability of FDA approved drug(s) for that kinase. Dark orange node outline dictates kinases which were down-selected in our binning analysis due to inconsistent phenotypes. Light orange node outline represents kinases which were down-selected in our binning analysis for having been studied in only one cell type or independent research study. The edges are colored grey by default. The edges of nodes with dark blue outlines (existing drugs) were colored respective to their node to visualize connectivity.

Figure 3.

Kinases mediate multiple stages of the DENV reproduction cycle. (A) DENV encounters host cells as an enveloped capsid containing a single-stranded, positive-sense RNA genome. The viral envelope (Env) attaches to the cell membrane via any of the plethora of identified DENV host receptors and is internalized primarily through clathrin-mediated endocytosis. Maturation of the endosome leads to conformational changes in Env that permits fusion of the viral envelope with the endosomal membrane followed by uncoating and release of the viral genome from the capsid. Subsequent translocation of the viral RNA to the rough endoplasmic reticulum allows for the coupled process of DENV genome replication and protein synthesis. DENV RNA is translated as a polyprotein encoding three structural proteins and seven non-structural. The newly produced viral genome and proteins are assembled into an immature virus particle which transits from the ER through the Trans-Golgi Network to undergo maturation via PrM cleavage. Mature, infectious virus egress from the cell through exocytosis. Kinase studies we reviewed (Supplementary Table 2) were assessed for information on activity during specific stages of DENV reproduction. The colored boxes overlayed on the cell list the kinases that were found to be involved in the specified stage of reproduction. This figure was partially created in https://BioRender.com. (B) Potential phosphosignaling pathways that link the kinases identified in (A) were investigated using PhosphoSitePlus and visualized with Cytoscape using the yFiles hierarchical layout. If a direct phosphorylation interaction between two of the input kinases does not occur, the shortest path of phosphorylation events that connects the two kinases is shown. Kinases with no interactions registered in PhosphoSitePlus are not shown. Kinase nodes were colored to indicate the stage of DENV reproduction they participate in. Nodes outlined in orange are kinases which have been shown to be important for dengue (Supplementary Table 2) but were not investigated at specific stages of infection. The references that informed this figure can be found in Supplementary Table 3.