Comparison of viral RNA\u2013host protein interactomes across pathogenic RNA viruses informs rapid antiviral drug discovery for SARS-CoV-2

Shaojun Zhang,Jian Rao,Lei Sun,Lili Ren,Xiaohui Ju,Qiangfeng Cliff Zhang,Mingli Gong,Qiang Ding,Wenze Huang,Pan Li,Jianwei Wang

doi:10.1038/s41422-021-00581-y

Abstract

In contrast to the extensive research about viral protein–host protein interactions that has revealed major insights about how RNA viruses engage with host cells during infection, few studies have examined interactions between host factors and viral RNAs (vRNAs). Here, we profiled vRNA–host protein interactomes for three RNA virus pathogens (SARS-CoV-2, Zika, and Ebola viruses) using ChIRP-MS. Comparative interactome analyses discovered both common and virus-specific host responses and vRNA-associated proteins that variously promote or restrict viral infection. In particular, SARS-CoV-2 binds and hijacks the host factor IGF2BP1 to stabilize vRNA and augment viral translation. Our interactome-informed drug repurposing efforts identified several FDA-approved drugs (e.g., Cepharanthine) as broad-spectrum antivirals in cells and hACE2 transgenic mice. A co-treatment comprising Cepharanthine and Trifluoperazine was highly potent against the newly emerged SARS-CoV-2 B.1.351 variant. Thus, our study illustrates the scientific and medical discovery utility of adopting a comparative vRNA–host protein interactome perspective.

Highlights

The SARS-CoV-2 coronavirus is the causal pathogen of the ongoing Coronavirus Disease 2019 (COVID-19) pandemic, resulting in more than 228 million infections and 4 million deaths and global disruption of society and economy.[1,2] SARS-CoV-2 is an RNA virus which relies heavily on interactions with host factor biomolecules to complete its life cycle.[3]
ChIRP-MS reveals viral RNAs (vRNAs)–host protein interactomes for SARSCoV-2, Zika, and Ebola viruses To discover the vRNA–host protein interactomes for SARS-CoV-2, EBOV, and Zika virus (ZIKV), we performed ChIRP-MS in virus-infected human host cells, using mock and vRNA segment transfection samples as controls (Fig. 1a; Materials and Methods)
We examined proteins previously reported to interact with EBOV vRNA (DHX9, hnRNPR, hnRNPL, SYNCRIP, IGF2BP1),[27] and confirmed that all these interactions are covered in our EBOV ChIRP-MS interactome (Fig. 2d, up; Supplementary information, Table S2)

Summary

Introduction

The SARS-CoV-2 coronavirus is the causal pathogen of the ongoing Coronavirus Disease 2019 (COVID-19) pandemic, resulting in more than 228 million infections and 4 million deaths and global disruption of society and economy.[1,2] SARS-CoV-2 is an RNA virus which relies heavily on interactions with host factor biomolecules to complete its life cycle.[3] RNA-binding proteins function in many aspects of cellular and viral processing, e.g., RNA translation, stabilization, modification, and localization.[4,5] Many studies have focused on characterization of viral protein–host protein interactions.[6,7,8,9,10] In contrast, interactions between host proteins and viral RNA (vRNA) are much less well understood, despite the known importance of the viral RNA genome for multiple processes during infection, including viral genome translation and replication.[11] Recent years have seen an explosion in high-throughput methods that enable global analyses of RNA–protein interactions (“the interactome”) in cells.[12,13] These approaches can substantially advance our understanding of the infection and pathology of RNA viruses and can inform diverse and effective therapeutic options. We showed that selective inhibition of host vRNA-binding proteins can attenuate infection and potently inform development of innovative therapies for viral infections including COVID-19

Methods

Results

Conclusion