Investigation of the Host Kinome Response to Coronavirus Infection Reveals PI3K/mTOR Inhibitors as Betacoronavirus Antivirals

Abstract

Host kinases play essential roles in the host cell cycle, innate immune signaling, the stress response to viral infection, and inflammation. Previous work has demonstrated that coronaviruses specifically target kinase cascades to subvert host cell responses to infection and rely upon host kinase activity to phosphorylate viral proteins to enhance replication. Given the number of kinase inhibitors that are already FDA approved to treat cancers, fibrosis, and other human disease, they represent an attractive class of compounds to repurpose for host-targeted therapies against emerging coronavirus infections. To further understand the host kinome response to betacoronavirus infection, we employed multiplex inhibitory bead mass spectrometry (MIB-MS) following MERS-CoV and SARS-CoV-2 infection of human lung epithelial cell lines. Our MIB-MS analyses revealed activation of mTOR and MAPK signaling following MERS-CoV and SARS-CoV-2 infection, respectively. SARS-CoV-2 host kinome responses were further characterized using paired phosphoproteomics, which identified activation of MAPK, PI3K, and mTOR signaling. Through chemogenomic screening, we found that clinically relevant PI3K/mTOR inhibitors were able to inhibit coronavirus replication at nanomolar concentrations similar to direct-acting antivirals. This study lays the groundwork for identifying broad-acting, hosttargeted therapies to reduce betacoronavirus replication that can be rapidly repurposed during future outbreaks and epidemics. The proteomics, phosphoproteomics, and MIB-MS datasets generated in this study are available in the Proteomics Identification Database (PRIDE) repository under project identifiers PXD040897 and PXD040901.

Time-based quantitative proteomic and phosphoproteomic analysis of A549-ACE2 cells during SARS-CoV-2 infection

“…Similarly, a Kinase Enrichment Analysis (KEA) of differential phosphopeptides at each time was performed to identify potential kinases whose regulation might lead to the observed changes in protein phosphorylation (Supplementary Figure 7 and Figure 3D). In agreement with previous reports, multiple kinases are activated upon SARS-CoV-2 infection of A549-ACE2 cells (24,26) which highlights a significant reprogramming of the cellular signaling landscape. Among them, CK2 (CSNK2A1) and CDKs may contribute to the regulation of viral replication (Figure 3D and Supplementary Figure 7).…”

On the origins of SARS-CoV-2 main protease inhibitors

“…150 Concerning other cellular kinases, a recent report has described far stronger in cellulo inhibition of SARS-CoV-2 replication by PI3K/mTOR inhibitors such as sapanisertib ( 40 ). 169 Future will tell if this translates into an in vivo effect although a precedent would be the inhibitors of cellular dihydroorotate dehydrogenase 170 which have yet to translate into effective RNA-based antivirals (including corona) in patients. 171–173 In 2004, niclosamide ( 41 ) was found to be endowed with a degree of antiviral effect on SARS-CoV-1 although it was not found to inhibit its main protease 174 and later on, this anthelminthic drug was also reported for its effect on many viruses, which has been recently reviewed.…”