The SARS-CoV‑2 Cytopathic Effect Is Blocked by Lysosome Alkalizing Small Molecules

Kirill Gorshkov, Catherine Z. Chen, Robert Bostwick, Lynn Rasmussen, Bruce Nguyen Tran, Yu-Shan Cheng, Miao Xu, Manisha Pradhan, Mark Henderson, Wei Zhu, Eunkeu Oh, Kimihiro Susumu, Mason Wolak, Khalida Shamim, Wenwei Huang, Xin Hu, Min Shen, Carleen Klumpp-Thomas, Zina Itkin, Paul Shinn, Juan Carlos de la Torre, Anton Simeonov, Sam G. Michael, Matthew D. Hall, Donald C. Lo, and Wei Zheng

Understanding the SARS-CoV-2 virus’ pathways of infection, virus−host−protein interactions, and mechanisms of virus-induced cytopathic effects will greatly aid in the discovery and design of new therapeutics to treat COVID-19. Chloroquine and hydroxychloroquine, extensively explored as clinical agents for COVID-19, have multiple cellular effects including alkalizing lysosomes and blocking autophagy as well as exhibiting dose-limiting toxicities in patients. Therefore, we evaluated additional lysosomotropic compounds to identify an alternative lysosome-based drug repurposing opportunity. We found that six of these compounds blocked the cytopathic effect of SARS-CoV-2 in Vero E6 cells with half-maximal effective concentration (EC50) values ranging from 2.0 to 13 μM and selectivity indices (SIs; SI = CC50/EC50) ranging from 1.5- to >10-fold. The compounds (1) blocked lysosome functioning and autophagy, (2) prevented pseudotyped particle entry, (3) increased lysosomal pH, and (4) reduced (ROC-325) viral titers in the EpiAirway 3D tissue model. Consistent with these findings, the siRNA knockdown of ATP6V0D1 blocked the HCoV-NL63 cytopathic effect in LLC-MK2 cells. Moreover, an analysis of SARS-CoV-2 infected Vero E6 cell lysate revealed significant dysregulation of autophagy and lysosomal function, suggesting a contribution of the lysosome to the life cycle of SARS-CoV-2. Our findings suggest the lysosome as a potential host cell target to combat SARS-CoV-2 infections and inhibitors of lysosomal function could become an important component of drug combination therapies aimed at improving treatment and outcomes for COVID-19.


SARS-CoV-2 virus, COVID-19, infection, viral replication, EpiAirway (AIR-100), lysosome alkalizing small molecules, viral titers, hydroxychloroquine, chloroquine, mefloquine, hycanthone, chlomipramine, verteporfin

Materials Tested

ROC-305, remdesivir, bleomycin

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