Virus–host interactomes — antiviral drug discovery

Abstract

One of the key questions in virology is how viruses, encoding relatively few genes, gain temporary or constant control over their hosts. To understand pathogenicity of a virus it is important to gain knowledge on the function of the individual viral proteins in the host cell, on their interactions with viral and cellular proteins and on the consequences of these interactions on cellular signaling pathways. A combination of transcriptomics, proteomics, high-throughput technologies and the bioinformatical analysis of the respective data help to elucidate specific cellular antiviral drug target candidates. In addition, viral and human interactome analyses indicate that different viruses target common, central human proteins for entering cellular signaling pathways and machineries which might constitute powerful broad-spectrum antiviral targets.

Antiviral drug discovery: broad-spectrum drugs from nature

“…Indeed, there are a number of chemical compounds that target common host factors and are at various levels of antiviral drug development (see under 3.2). In addition, with the advent of better screening technologies, we now know that the number of host factors associated with viral replication is strikingly large [64][65][66][67] . This provides a vast space to explore further antiviral targets 68 .…”

Recent advances in host–virus interactomics during entry and infection

“…21 The study of virus-host PPIs has been possible through binary Y2H assays or complex affinity purification followed by MS. 22 However, the Y2H system of detection of virus-host PPIs has few formidable limitations: frequent false positives; limitation of analysis of hydrophobic membrane proteins, owing to the expression of the reporter system within the nuclei; and lack of mammalian posttranslational modifications in yeast. 20 Several strategies have been developed in order to overcome these limitations, such as the use of novel N-terminal bait and C-terminal bait and prey fusion-protein vectors, validation of Y2H data through biochemical and/or cell-based assays, and co-immunoprecipitation studies. In HT-Y2H assays, the limitations discussed above have been addressed through several ingenuous study designs, such as the LUminescencebased Mammalian IntERactome (LUMIER) mapping, and other variations of luminescence-based protein-fragment complementation assays, eg, split-yellow fluorescent protein (YFP) or split-luciferase-based methods.…”

“…27 Systematic Y2H virus-host interaction screens, which are subsequently validated by a variety of methods, have been used to chart several virus-host PPIs, such as in HCV, Epstein-Barr virus (EBV), KSHV and varicella-zoster virus (VZV), dengue virus (DENV), and HIV-1. 20,[28][29][30][31][32] Chikungunya virus (CHIKV; family Togaviridae)-host-protein interactions have been investigated through HT-Y2H assays that are validated by protein interaction mapping. 33 Out of …”

“…2D gel electrophoresis of wholecell lysates taken before and after infection followed by mass spectrometry (MS) identified the proteins detected in a gel. 19,20 High-throughput yeast two-hybrid (HT-Y2H) assays have been useful in exploring protein-protein interactions (PPIs) in Saccharomyces cerevisiae using full-length predicted open reading frames. 21 The study of virus-host PPIs has been possible through binary Y2H assays or complex affinity purification followed by MS. 22 However, the Y2H system of detection of virus-host PPIs has few formidable limitations: frequent false positives; limitation of analysis of hydrophobic membrane proteins, owing to the expression of the reporter system within the nuclei; and lack of mammalian posttranslational modifications in yeast.…”

“…35 The involvement of ribosome in host mRNA degradation (influenza virus and SARS-CoV), vATPase in pH-dependent endosomal release (SARS-CoV, Semliki Forest virus; family Togaviridae), and nuclear pore-associated protein such as human KPNA1 (Karyopherin alpha 1 or importin alpha 5) and MAPK-signaling pathway in infections of SARS-CoV and HCV has been elucidated through these studies. 20 The study of HIV-human protein interaction by Jäger et al employed affinity tagging and purification followed by MS that revealed several interactions of HIV-1 proteins in two human cell lines (HEK293 and Jurkat). 36 The authors scored the PPIs using an improvised scoring system (MS interaction statistics) and plotted 497 HIV-human PPIs involving 435 individual human proteins in an interaction map.…”