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

Denisa Bojkova; Philipp Reus; Leona Panosch; Marco Bechtel; Tamara Rothenburger; Joshua D. Kandler; Annika Pfeiffer; Julian U.G. Wagner; Mariana Shumliakivska; Stefanie Dimmeler; Ruth Olmer; Ulrich Martin; Florian W.R. Vondran; Tuna Toptan; Florian Rothweiler; Richard Zehner; Holger F. Rabenau; Karen L. Osman; Steven T. Pullan; Miles W. Carroll; Richard Stack; Sandra Ciesek; Mark N. Wass; Martin Michaelis; Jindrich Cinatl

doi:10.1016/j.isci.2023.105944

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

Denisa Bojkova, Philipp Reus, Leona Panosch, Marco Bechtel, Tamara Rothenburger, Joshua D. Kandler, Annika Pfeiffer, Julian U.G. Wagner, Mariana Shumliakivska, Stefanie Dimmeler, Ruth Olmer, Ulrich Martin, Florian W.R. Vondran, Tuna Toptan, Florian Rothweiler, Richard Zehner, Holger F. Rabenau, Karen L. Osman, Steven T. Pullan, Miles W. CarrollRichard Stack, Sandra Ciesek, Mark N. Wass, Martin Michaelis^*, Jindrich Cinatl^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

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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 readout 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 1,796 kinase inhibitors identified known and novel antiviral drug candidates including inhibitors of phosphoglycerate dehydrogenase (PHGDH), CDC like kinase 1 (CLK-1), and colony stimulating factor 1 receptor (CSF1R). The activity of the PHGDH inhibitor NCT-503 was further increased in combination with the hexokinase II (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.

Original language	English
Article number	105944
Journal	iScience
Volume	26
Issue number	2
Early online date	11 Jan 2023
DOIs	https://doi.org/10.1016/j.isci.2023.105944
Publication status	Published - 17 Feb 2023

Bibliographical note

Funding Information:nWe thank Kerstin Euler, Sebastian Grothe, and Lena Stegman for their technical assistance. This work was supported by the Frankfurter Stiftung für krebskranke Kinder , the Goethe-Corona-Fonds, BMBF (COVID-Protect), the Corona Accelerated R&D in Europe ( CARE ) project from the Innovative Medicines Initiative 2 Joint Undertaking (JU) under grant agreement No 101005077 , and the BBSRC (SoCoBio DTP training program).

Open Access: This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

Publisher Copyright: © 2023 The Authors.

Citation: Denisa Bojkova, Philipp Reus, Leona Panosch, Marco Bechtel, Tamara Rothenburger, Joshua D. Kandler, Annika Pfeiffer, Julian U.G. Wagner, Mariana Shumliakivska, Stefanie Dimmeler, Ruth Olmer, Ulrich Martin, Florian W.R. Vondran, Tuna Toptan, Florian Rothweiler, Richard Zehner, Holger F. Rabenau, Karen L. Osman, Steven T. Pullan, Miles W. Carroll, Richard Stack, Sandra Ciesek, Mark N. Wass, Martin Michaelis, Jindrich Cinatl, Identification of novel antiviral drug candidates using an optimized SARS-CoV-2 phenotypic screening platform, iScience, Volume 26, Issue 2, 2023, 105944, ISSN 2589-0042, https://doi.org/10.1016/j.isci.2023.105944.

DOI: https://doi.org/10.1016/j.isci.2023.105944

Keywords

Drugs
Screening in health technology
Virology

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10.1016/j.isci.2023.105944Licence: CC BY-NC-ND

Bojkova2023IdentificationOfNovelAntiviralDrugCandidatesUsingAnOptimizedSARS-CoV-2PhenotypicScreeningPlatformiScienceFinal published version, 5.7 MBLicence: CC BY-NC-ND

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Bojkova, D., Reus, P., Panosch, L., Bechtel, M., Rothenburger, T., Kandler, J. D., Pfeiffer, A., Wagner, J. U. G., Shumliakivska, M., Dimmeler, S., Olmer, R., Martin, U., Vondran, F. W. R., Toptan, T., Rothweiler, F., Zehner, R., Rabenau, H. F., Osman, K. L., Pullan, S. T., ... Cinatl, J. (2023). Identification of novel antiviral drug candidates using an optimized SARS-CoV-2 phenotypic screening platform. iScience, 26(2), Article 105944. https://doi.org/10.1016/j.isci.2023.105944

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title = "Identification of novel antiviral drug candidates using an optimized SARS-CoV-2 phenotypic screening platform",

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 readout 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 1,796 kinase inhibitors identified known and novel antiviral drug candidates including inhibitors of phosphoglycerate dehydrogenase (PHGDH), CDC like kinase 1 (CLK-1), and colony stimulating factor 1 receptor (CSF1R). The activity of the PHGDH inhibitor NCT-503 was further increased in combination with the hexokinase II (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 = "Drugs, Screening in health technology, Virology",

author = "Denisa Bojkova and Philipp Reus and Leona Panosch and Marco Bechtel and Tamara Rothenburger and Kandler, {Joshua D.} and Annika Pfeiffer and Wagner, {Julian U.G.} and Mariana Shumliakivska and Stefanie Dimmeler and Ruth Olmer and Ulrich Martin and Vondran, {Florian W.R.} and Tuna Toptan and Florian Rothweiler and Richard Zehner and Rabenau, {Holger F.} and Osman, {Karen L.} and Pullan, {Steven T.} and Carroll, {Miles W.} and Richard Stack and Sandra Ciesek and Wass, {Mark N.} and Martin Michaelis and Jindrich Cinatl",

note = "Funding Information:nWe thank Kerstin Euler, Sebastian Grothe, and Lena Stegman for their technical assistance. This work was supported by the Frankfurter Stiftung f{\"u}r krebskranke Kinder , the Goethe-Corona-Fonds, BMBF (COVID-Protect), the Corona Accelerated R&D in Europe ( CARE ) project from the Innovative Medicines Initiative 2 Joint Undertaking (JU) under grant agreement No 101005077 , and the BBSRC (SoCoBio DTP training program). Open Access: This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). Publisher Copyright: {\textcopyright} 2023 The Authors. Citation: Denisa Bojkova, Philipp Reus, Leona Panosch, Marco Bechtel, Tamara Rothenburger, Joshua D. Kandler, Annika Pfeiffer, Julian U.G. Wagner, Mariana Shumliakivska, Stefanie Dimmeler, Ruth Olmer, Ulrich Martin, Florian W.R. Vondran, Tuna Toptan, Florian Rothweiler, Richard Zehner, Holger F. Rabenau, Karen L. Osman, Steven T. Pullan, Miles W. Carroll, Richard Stack, Sandra Ciesek, Mark N. Wass, Martin Michaelis, Jindrich Cinatl, Identification of novel antiviral drug candidates using an optimized SARS-CoV-2 phenotypic screening platform, iScience, Volume 26, Issue 2, 2023, 105944, ISSN 2589-0042, https://doi.org/10.1016/j.isci.2023.105944. DOI: https://doi.org/10.1016/j.isci.2023.105944",

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doi = "10.1016/j.isci.2023.105944",

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Bojkova, D, Reus, P, Panosch, L, Bechtel, M, Rothenburger, T, Kandler, JD, Pfeiffer, A, Wagner, JUG, Shumliakivska, M, Dimmeler, S, Olmer, R, Martin, U, Vondran, FWR, Toptan, T, Rothweiler, F, Zehner, R, Rabenau, HF, Osman, KL, Pullan, ST, Carroll, MW, Stack, R, Ciesek, S, Wass, MN, Michaelis, M & Cinatl, J 2023, 'Identification of novel antiviral drug candidates using an optimized SARS-CoV-2 phenotypic screening platform', iScience, vol. 26, no. 2, 105944. https://doi.org/10.1016/j.isci.2023.105944

TY - JOUR

T1 - Identification of novel antiviral drug candidates using an optimized SARS-CoV-2 phenotypic screening platform

AU - Bojkova, Denisa

AU - Reus, Philipp

AU - Panosch, Leona

AU - Bechtel, Marco

AU - Rothenburger, Tamara

AU - Kandler, Joshua D.

AU - Pfeiffer, Annika

AU - Wagner, Julian U.G.

AU - Shumliakivska, Mariana

AU - Dimmeler, Stefanie

AU - Olmer, Ruth

AU - Martin, Ulrich

AU - Vondran, Florian W.R.

AU - Toptan, Tuna

AU - Rothweiler, Florian

AU - Zehner, Richard

AU - Rabenau, Holger F.

AU - Osman, Karen L.

AU - Pullan, Steven T.

AU - Carroll, Miles W.

AU - Stack, Richard

AU - Ciesek, Sandra

AU - Wass, Mark N.

AU - Michaelis, Martin

AU - Cinatl, Jindrich

N1 - Funding Information:nWe thank Kerstin Euler, Sebastian Grothe, and Lena Stegman for their technical assistance. This work was supported by the Frankfurter Stiftung für krebskranke Kinder , the Goethe-Corona-Fonds, BMBF (COVID-Protect), the Corona Accelerated R&D in Europe ( CARE ) project from the Innovative Medicines Initiative 2 Joint Undertaking (JU) under grant agreement No 101005077 , and the BBSRC (SoCoBio DTP training program). Open Access: This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/). Publisher Copyright: © 2023 The Authors. Citation: Denisa Bojkova, Philipp Reus, Leona Panosch, Marco Bechtel, Tamara Rothenburger, Joshua D. Kandler, Annika Pfeiffer, Julian U.G. Wagner, Mariana Shumliakivska, Stefanie Dimmeler, Ruth Olmer, Ulrich Martin, Florian W.R. Vondran, Tuna Toptan, Florian Rothweiler, Richard Zehner, Holger F. Rabenau, Karen L. Osman, Steven T. Pullan, Miles W. Carroll, Richard Stack, Sandra Ciesek, Mark N. Wass, Martin Michaelis, Jindrich Cinatl, Identification of novel antiviral drug candidates using an optimized SARS-CoV-2 phenotypic screening platform, iScience, Volume 26, Issue 2, 2023, 105944, ISSN 2589-0042, https://doi.org/10.1016/j.isci.2023.105944. DOI: https://doi.org/10.1016/j.isci.2023.105944

PY - 2023/2/17

Y1 - 2023/2/17

N2 - 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 readout 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 1,796 kinase inhibitors identified known and novel antiviral drug candidates including inhibitors of phosphoglycerate dehydrogenase (PHGDH), CDC like kinase 1 (CLK-1), and colony stimulating factor 1 receptor (CSF1R). The activity of the PHGDH inhibitor NCT-503 was further increased in combination with the hexokinase II (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.

AB - 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 readout 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 1,796 kinase inhibitors identified known and novel antiviral drug candidates including inhibitors of phosphoglycerate dehydrogenase (PHGDH), CDC like kinase 1 (CLK-1), and colony stimulating factor 1 receptor (CSF1R). The activity of the PHGDH inhibitor NCT-503 was further increased in combination with the hexokinase II (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.

KW - Drugs

KW - Screening in health technology

KW - Virology

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JO - iScience

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

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