Click. Screen. Degrade. A Miniaturized D2B Workflow for rapid PROTAC Discovery

Mitrovic, M.; Greco, F. A.; Garcia, Y. C.; Lucic, A.; Hoffmann, L.; Chander, R.; Schoenfeld, J.; Liebisch, N.; Schwalm, M. P.; Egner, M.; Lewandowski, M.; Merk, D.; Morasch, V.; Wolf, E.; Mueller, S.; Hanke, T.; Proschak, E.; Hiesinger, K.; Knapp, S.

doi:10.1101/2025.07.29.667383

bioRxiv · 10.1101/2025.07.29.667383

Click. Screen. Degrade. A Miniaturized D2B Workflow for rapid PROTAC Discovery

Mitrovic, M.·Greco, F. A.·Garcia, Y. C.·Lucic, A.·Hoffmann, L.·Chander, R.·Schoenfeld, J.·Liebisch, N.·Schwalm, M. P.·Egner, M.·Lewandowski, M.·Merk, D.·Morasch, V.·Wolf, E.·Mueller, S.·Hanke, T.·Proschak, E.·Hiesinger, K.·Knapp, S.

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Abstract

Targeted protein degradation is one of the fastest developing fields in medicinal chemistry and chemical biology. Despite significant development in assay technologies and inhibitor discovery, the development of PROTACs remains a challenging endeavor since rational design approaches remain widely elusive. Our workflow eliminates the rate-limiting step of classic synthesis, namely compound purification, and pairs it with high-throughput, semi-automated plate-based synthesis, and direct cellular assay evaluation. We applied this direct-to-biology approach to four diverse targets demonstrating the general applicability of this technology. PROTAC synthesis was realized by using the highly efficient copper-catalyzed azide-alkyne cycloaddition reaction. This simplified reaction setup allowed synthesis in the nanomole scale with reaction volumes as low as 5 L. This high throughput approach enables the synthesis and testing of hundreds of PROTACs within a few days, allowing for a comprehensive assessment of target degradability and the identification of the most suitable E3 ligase for degrader development.

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Mitrovic, M., Greco, F. A., Garcia, Y. C., Lucic, A., Hoffmann, L., Chander, R., Schoenfeld, J., Liebisch, N., Schwalm, M. P., Egner, M., Lewandowski, M., Merk, D., Morasch, V., Wolf, E., Mueller, S., Hanke, T., Proschak, E., Hiesinger, K., Knapp, S.. 2025-07-31. Click. Screen. Degrade. A Miniaturized D2B Workflow for rapid PROTAC Discovery. https://doi.org/10.1101/2025.07.29.667383

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