SARS‐CoV‐2–host proteome interactions for antiviral drug discovery

Abstract

Treatment options for COVID-19, caused by SARS-CoV-2, remain limited. Understanding viral pathogenesis at the molecular level is critical to develop effective therapy. Some recent studies have explored SARS-CoV-2-host interactomes and provided great resources for understanding viral replication. However, host proteins that functionally associate with SARS-CoV-2 are localized in the corresponding subnetwork within the comprehensive human interactome. Therefore, constructing a downstream network including all potential viral receptors, host cell proteases, and cofactors is necessary and should be used as an additional criterion for the validation of critical host machineries used for viral processing. This study applied both affinity purification mass spectrometry (AP-MS) and the complementary proximity-based labeling MS method (BioID-MS) on 29 viral ORFs and 18 host proteins with potential roles in viral replication to map the interactions relevant to viral processing. The analysis yields a list of 693 hub proteins sharing interactions with both viral baits and host baits and revealed their biological significance for SARS-CoV-2. Those hub proteins then served as a rational resource for drug repurposing via a virtual screening approach. The overall process resulted in the suggested repurposing of 59 compounds for 15 protein targets. Furthermore, antiviral effects of some candidate drugs were observed in vitro validation using image-based drug screen with infectious SARS-CoV-2. In addition, our results suggest that the antiviral activity of methotrexate could be associated with its inhibitory effect on specific protein-protein interactions.

A BioID-Derived Proximity Interactome for SARS-CoV-2 Proteins

“…In order to develop a high-confidence list of viral-host PPIs, we compared our BioID dataset to three previously published proximity-labeling datasets [ 14 , 15 , 22 ]. “High confidence interactions” were those that were identified in at least three studies and four datasets, with degree of connection ≤ 3 for at least four datasets.…”

“…Datasets were obtained from three separate studies [ 14 , 15 , 22 ]. Interactions deemed significant by respective authors were compiled in one excel spreadsheet without filtering out preys identified across multiple baits.…”

“…A crucial component of the effort to study COVID-19 is the application of technologies that reveal how viral proteins behave in host cells. Current efforts to map the SARS-CoV-2 virus-host interactome have offered great insight into possible pathways directly affected by various viral proteins, yet differences in experimental approaches and data analysis methods inevitably lead to discrepancies when comparing reported interactomes [ 11 , 12 , 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 ]. As with any large-scale approach to identifying gene or protein networks, false positives due to background contamination can hinder accurate data interpretation; therefore, the use of several approaches with multiple replicates by multiple independent studies will be required to ultimately map the full SARS-CoV-2 interactome.…”

The ACE2 Receptor for Coronavirus Entry Is Localized at Apical Cell—Cell Junctions of Epithelial Cells

“…Interestingly, both NHERF1 and SNX27 also modulate TJ organization and barrier function, by associating with the TJ protein ZO-2 (SNX27) and regulating cytoskeletal organization and membrane trafficking [ 84 , 85 ]. Finally, proximity label mass spectrometry analysis identifies occludin as proximal to ACE2 (ACE2 BioGrid data, [ 86 ]). Together, these observations further reinforce the notion of a mechanistic link between TJ membrane and scaffolding proteins, ACE2 and SARS-CoV-2 entry.…”

Open modification searching of SARS-CoV-2–human protein interaction data reveals novel viral modification sites

“…The majority of previously conducted studies use standard sequence database searching to process AP-MS data [2, 7-10]. Most search engines require the user to explicitly specify potential protein modifications to be considered during searching.…”