PIP4K2C inhibition reverses autophagic flux impairment induced by SARS-CoV-2
Marwah Karim, Manjari Mishra, Chieh‐Wen Lo, Sirle Saul, H. Busra Cagirici, Manon Gourdelier, Luca Ghita, Amrita Ojha, Tran Do Hoang Nhu, Aditi Agrawal, Connor McGraw, Michael P. East, Karen Anbro Gammeltoft, Malaya K. Sahoo, Nancie A. Mooney, Gary L. Johnson, Soumita Das, Pieter Leyssen, Johan Neyts, Winston Chiu, Courtney A. Cohen, Jens Bukh, Judith M. Gottwein, John M. Dye, Norma Neff, Peter K. Jackson, Benjamin A. Pinsky, Tuomo Laitinen, Tatu Pantsar, Antti Poso, Fabio Zanini, Steven De Jonghe, Christopher R. M. Asquith, Shirit Einav
Abstract
In search for broad-spectrum antivirals, we discover a small molecule inhibitor, RMC-113, that potently suppresses the replication of multiple RNA viruses including SARS-CoV-2 in human lung organoids. We demonstrate selective inhibition of the lipid kinases PIP4K2C and PIKfyve by RMC-113 and target engagement by its clickable analog. Lipidomics analysis reveals alteration of SARS-CoV-2-induced phosphoinositide signature by RMC-113 and links its antiviral effect with functional PIP4K2C and PIKfyve inhibition. We identify PIP4K2C’s roles in SARS-CoV-2 entry, RNA replication, and assembly/egress, validating it as a druggable antiviral target. Integrating proteomics, single-cell transcriptomics, and functional assays, reveals that PIP4K2C binds SARS-CoV-2 nonstructural protein 6 and regulates virus-induced autophagic flux impairment. Promoting viral protein degradation by reversing autophagic flux impairment is a mechanism of antiviral action of RMC-113. These findings reveal virus-induced autophagy regulation via PIP4K2C, an understudied kinase, and propose dual PIP4K2C and PIKfyve inhibition as a candidate strategy to combat emerging viruses. The understudied lipid kinase PIP4K2C binds SARS-CoV-2 nonstructural protein 6 and regulates virus-induced autophagic flux impairment, suppressing viral protein degradation. PIP4K2C inhibition is a candidate strategy to combat emerging viruses.