iScience . Identification of novel antiviral drug candidates using an optimized SARS-CoV-2 phenotypic screening platform

[tetano]

iScience


. 2023 Jan 7;105944.
doi: 10.1016/j.isci.2023.105944. Online ahead of print.
Identification of novel antiviral drug candidates using an optimized SARS-CoV-2 phenotypic screening platform


Denisa Bojkova ¹ , Philipp Reus ^{1 2} , Leona Panosch ¹ , Marco Bechtel ¹ , Tamara Rothenburger ¹ , Joshua D Kandler ¹ , Annika Pfeiffer ¹ , Julian U G Wagner ^{3 4 5} , Mariana Shumliakivska ³ , Stefanie Dimmeler ^{3 4 5} , Ruth Olmer ⁶ , Ulrich Martin ⁶ , Florian W R Vondran ^{7 8} , Tuna Toptan ¹ , Florian Rothweiler ^{1 9} , Richard Zehner ¹⁰ , Holger F Rabenau ¹ , Karen L Osman ¹¹ , Steven T Pullan ¹¹ , Miles W Carroll ^{12 13} , Richard Stack ¹⁴ , Sandra Ciesek ^{1 2 8} , Mark N Wass ¹⁴ , Martin Michaelis ¹⁴ , Jindrich Cinatl Jr ^{1 9}



Affiliations

• PMID: 36644320
• PMCID: PMC9822553
• DOI: 10.1016/j.isci.2023.105944

Abstract

Reliable, easy-to-handle phenotypic screening platforms are needed for the identification of anti-SARS-CoV-2 compounds. Here, we present caspase 3/7 activity as a read-out for monitoring the replication of SARS-CoV-2 isolates from different variants, including a remdesivir-resistant strain, and of other coronaviruses in numerous cell culture models, independently of cytopathogenic effect formation. Compared to other models, the Caco-2 subline Caco-2-F03 displayed superior performance. It possesses a stable SARS-CoV-2 susceptibility phenotype and does not produce false-positive hits due to drug-induced phospholipidosis. A proof-of-concept screen of 1796 kinase inhibitors identified known and novel antiviral drug candidates including inhibitors of PHGDH, CLK-1, and CSF1R. The activity of the PHGDH inhibitor NCT-503 was further increased in combination with the HK2 inhibitor 2-deoxy-D-glucose, which is in clinical development for COVID-19. In conclusion, caspase 3/7 activity detection in SARS-CoV-2-infected Caco-2-F03 cells provides a simple phenotypic high-throughput screening platform for SARS-CoV-2 drug candidates that reduces false positive hits.

Keywords: COVID-19; Caco-2-F03; SARS-CoV-2; antiviral therapy; drug discovery.