Discovery of potent SARS-CoV-2 nsp3 macrodomain inhibitors uncovers lack of translation to cellular antiviral response

Lee, A. A.; Amick, I.; Aschenbrenner, J. C.; Barr, H. A.; Benjamin, J.; Brandis, A.; Cohen, G.; Diaz-Tapia, R.; Duberstein, S.; Dixon, J.; Cousins, D.; Fairhead, M.; Fearon, D.; Frick, J.; Gayvert, J.; de Godoy, A. S.; Griffen, E. J.; Huber, K. V. M.; Koekemoer, L.; Lahav, N.; Marples, P. G.; McGovern, B. L.; Mehlman, T.; Robinson, M. C.; Singh, U.; Szommer, T.; Tomlinson, C. W. E.; Vargo, T.; von Delft, F.; Wang, S.; White, K. M.; Williams, E.; Winokan, M.

doi:10.1101/2024.08.19.608619

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bioRxiv · 10.1101/2024.08.19.608619

Discovery of potent SARS-CoV-2 nsp3 macrodomain inhibitors uncovers lack of translation to cellular antiviral response

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Abstract

A strategy for pandemic preparedness is the development of antivirals against a wide set of viral targets with complementary mechanisms of action. SARS-CoV-2 nsp3-mac1 is a viral macrodomain with ADP-ribosylhydrolase activity, which counteracts host immune response. Targeting the virus immunomodulatory functionality offers a differentiated strategy to inhibit SARS-CoV-2 compared to approved therapeutics, which target viral replication directly. Here we report a fragment-based lead generation campaign guided by computational approaches. We discover tool compounds which inhibit nsp3-mac1 activity at low nanomolar concentrations, and with responsive structure-activity relationships, high selectivity, and drug-like properties. Using our inhibitors, we show that inhibition of nsp3-mac1 increases ADP-ribosylation, but surprisingly does not translate to demonstrable antiviral activity in cell culture and iPSC-derived pneumocyte models. Further, no synergistic activity is observed in combination with interferon gamma, a main protease inhibitor, nor a papain-like protease inhibitor. Our results question the extent to which targeting modulation of innate immunity-driven ADP-ribosylation can influence SARS-CoV-2 replication. Moreover, these findings suggest that nsp3-mac1 might not be a suitable target for antiviral therapeutics development.

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Lee, A. A., Amick, I., Aschenbrenner, J. C., Barr, H. A., Benjamin, J., Brandis, A., Cohen, G., Diaz-Tapia, R., Duberstein, S., Dixon, J., Cousins, D., Fairhead, M., Fearon, D., Frick, J., Gayvert, J., de Godoy, A. S., Griffen, E. J., Huber, K. V. M., Koekemoer, L., Lahav, N., Marples, P. G., McGovern, B. L., Mehlman, T., Robinson, M. C., Singh, U., Szommer, T., Tomlinson, C. W. E., Vargo, T., von Delft, F., Wang, S., White, K. M., Williams, E., Winokan, M.. 2024-08-21. Discovery of potent SARS-CoV-2 nsp3 macrodomain inhibitors uncovers lack of translation to cellular antiviral response. https://doi.org/10.1101/2024.08.19.608619

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