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Bakowski MA, Beutler N, Wolff KC, Kirkpatrick MG, Chen E, Nguyen TTH, Riva L, Shaabani N, Parren M, Ricketts J, Gupta AK, Pan K, Kuo P, Fuller M, Garcia E, Teijaro JR, Yang L, Sahoo D, Chi V, Huang E, Vargas N, Roberts AJ, Das S, Ghosh P, Woods AK, Joseph SB, Hull MV, Schultz PG, Burton DR, Chatterjee AK, McNamara CW, Rogers TF. Drug repurposing screens identify chemical entities for the development of COVID-19 interventions. Nat Commun 2021; 12:3309. [PMID: 34083527 PMCID: PMC8175350 DOI: 10.1038/s41467-021-23328-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 04/19/2021] [Indexed: 12/15/2022] Open
Abstract
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.
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Affiliation(s)
- Malina A Bakowski
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA.
| | - Nathan Beutler
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Karen C Wolff
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | | | - Emily Chen
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Tu-Trinh H Nguyen
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Laura Riva
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Namir Shaabani
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Mara Parren
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - James Ricketts
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Anil K Gupta
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Kastin Pan
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Peiting Kuo
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - MacKenzie Fuller
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA
- HUMANOID CoRE, UC San Diego, La Jolla, CA, USA
| | - Elijah Garcia
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - John R Teijaro
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Linlin Yang
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Debashis Sahoo
- Department of Computer Science and Engineering, Jacobs School of Engineering, UC San Diego, La Jolla, CA, USA
- Department of Pediatrics, UC San Diego, La Jolla, CA, USA
| | - Victor Chi
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Edward Huang
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Natalia Vargas
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Amanda J Roberts
- Animal Models Core Facility, The Scripps Research Institute, La Jolla, CA, USA
| | - Soumita Das
- HUMANOID CoRE, UC San Diego, La Jolla, CA, USA
- Department of Pathology, UC San Diego, La Jolla, CA, USA
| | - Pradipta Ghosh
- Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA
- HUMANOID CoRE, UC San Diego, La Jolla, CA, USA
- Department of Medicine, UC San Diego, La Jolla, CA, USA
| | - Ashley K Woods
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Sean B Joseph
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Mitchell V Hull
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Peter G Schultz
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | | | - Case W McNamara
- Calibr, a division of The Scripps Research Institute, La Jolla, CA, USA
| | - Thomas F Rogers
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
- UC San Diego Division of Infectious Diseases and Global Public Health, UC San Diego School of Medicine, La Jolla, CA, USA.
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