- Bakowski, Malina A;
- Beutler, Nathan;
- Wolff, Karen C;
- Kirkpatrick, Melanie G;
- Chen, Emily;
- Nguyen, Tu-Trinh H;
- Riva, Laura;
- Shaabani, Namir;
- Parren, Mara;
- Ricketts, James;
- Gupta, Anil K;
- Pan, Kastin;
- Kuo, Peiting;
- Fuller, MacKenzie;
- Garcia, Elijah;
- Teijaro, John R;
- Yang, Linlin;
- Sahoo, Debashis;
- Chi, Victor;
- Huang, Edward;
- Vargas, Natalia;
- Roberts, Amanda J;
- Das, Soumita;
- Ghosh, Pradipta;
- Woods, Ashley K;
- Joseph, Sean B;
- Hull, Mitchell V;
- Schultz, Peter G;
- Burton, Dennis R;
- Chatterjee, Arnab K;
- McNamara, Case W;
- Rogers, Thomas F
The ongoing pandemic caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), necessitates strategies to identify prophylactic and therapeutic drug candidates for rapid clinical deployment. Here, we describe a screening pipeline for the discovery of efficacious SARS-CoV-2 inhibitors. We screen a best-in-class drug repurposing library, ReFRAME, against two high-throughput, high-content imaging infection assays: one using HeLa cells expressing SARS-CoV-2 receptor ACE2 and the other using lung epithelial Calu-3 cells. From nearly 12,000 compounds, we identify 49 (in HeLa-ACE2) and 41 (in Calu-3) compounds capable of selectively inhibiting SARS-CoV-2 replication. Notably, most screen hits are cell-line specific, likely due to different virus entry mechanisms or host cell-specific sensitivities to modulators. Among these promising hits, the antivirals nelfinavir and the parent of prodrug MK-4482 possess desirable in vitro activity, pharmacokinetic and human safety profiles, and both reduce SARS-CoV-2 replication in an orthogonal human differentiated primary cell model. Furthermore, MK-4482 effectively blocks SARS-CoV-2 infection in a hamster model. Overall, we identify direct-acting antivirals as the most promising compounds for drug repurposing, additional compounds that may have value in combination therapies, and tool compounds for identification of viral host cell targets.