The FDA-approved drug Alectinib compromises SARS-CoV-2 nucleocapsid phosphorylation and inhibits viral infection in vitro

Yaron, Tomer M.; Heaton, Brook E.; Levy, Tyler M.; Johnson, Jared L.; Jordan, Tristan X.; Cohen, Benjamin M.; Kerelsky, Alexander; Lin, Ting-Yu; Liberatore, Katarina M.; Bulaon, Danielle K.; Kastenhuber, Edward R.; Mercadante, Marisa N.; Shobana-Ganesh, Kripa; He, Long; Schwartz, Robert E.; Chen, Shuibing; Weinstein, Harel; Elemento, Olivier; Piskounova, Elena; Nilsson-Payant, Benjamin E.; Lee, Gina; Trimarco, Joseph D.; Burke, Kaitlyn N.; Hamele, Cait E.; Chaparian, Ryan R.; Harding, Alfred T.; Tata, Aleksandra; Zhu, Xinyu; Tata, Purushothama Rao; Smith, Clare M.; Possemato, Anthony P.; Tkachev, Sasha L.; Hornbeck, Peter V.; Beausoleil, Sean A.; Anand, Shankara K.; Aguet, François; Getz, Gad; Davidson, Andrew D.; Heesom, Kate; Kavanagh-Williamson, Maia; Matthews, David; tenOever, Benjamin R.; Cantley, Lewis C.; Blenis, John; Heaton, Nicholas S.

While vaccines are vital for preventing COVID-19 infections, it is critical to develop new therapies to treat patients who become infected. Pharmacological targeting of a host factor required for viral replication can suppress viral spread with a low probability of viral mutation leading to resistance. In particular, host kinases are highly druggable targets and a number of conserved coronavirus proteins, notably the nucleoprotein (N), require phosphorylation for full functionality. In order to understand how targeting kinases could be used to compromise viral replication, we used a combination of phosphoproteomics and bioinformatics as well as genetic and pharmacological kinase inhibition to define the enzymes important for SARS-CoV-2 N protein phosphorylation and viral replication. From these data, we propose a model whereby SRPK1/2 initiates phosphorylation of the N protein, which primes for further phosphorylation by GSK-3α/β and CK1 to achieve extensive phosphorylation of the N protein SR-rich domain. Importantly, we were able to leverage our data to identify an FDA-approved kinase inhibitor, Alectinib, that suppresses N phosphorylation by SRPK1/2 and limits SARS-CoV-2 replication. Together, these data suggest that repurposing or developing novel host-kinase directed therapies may be an efficacious strategy to prevent or treat COVID-19 and other coronavirus-mediated diseases.