Back-pocket optimization of 2-aminopyrimidine-based macrocycles leads to potent dual EPHA2/GAK kinase inhibitors with antiviral activity

Gerninghaus, J.; Zhubi, R.; Kraemer, A.; Karim, M.; Tran, D. H. N.; Joerger, A. C.; Schreiber, C.; Berger, L. M.; Berger, B. T.; Ehret, T. A. L.; Elson, L.; Lenz, C.; Saxena, K.; Mueller, S.; Einav, S.; Knapp, S.; Hanke, T.

doi:10.1101/2024.02.18.580805

bioRxiv · 10.1101/2024.02.18.580805

Back-pocket optimization of 2-aminopyrimidine-based macrocycles leads to potent dual EPHA2/GAK kinase inhibitors with antiviral activity

Gerninghaus, J.·Zhubi, R.·Kraemer, A.·Karim, M.·Tran, D. H. N.·Joerger, A. C.·Schreiber, C.·Berger, L. M.·Berger, B. T.·Ehret, T. A. L.·Elson, L.·Lenz, C.·Saxena, K.·Mueller, S.·Einav, S.·Knapp, S.·Hanke, T.

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Abstract

Macrocyclization of acyclic compounds is a powerful strategy for improving inhibitor potency and selectivity. Here, we developed a 2-aminopyrimidine-based macrocyclic dual EPHA2/GAK kinase inhibitor as a chemical tool to study the role of these two kinases in viral entry and assembly. Starting with a promiscuous macrocyclic inhibitor, 6, we performed a structure-guided activity relationship and selectivity study using a panel of over 100 kinases. The crystal structure of EPHA2 in complex with the developed macrocycle 23 provided a basis for further optimization by specifically targeting the back pocket, resulting in compound 55 as a potent dual EPHA2/GAK inhibitor. Subsequent front-pocket derivatization resulted in an interesting in cellulo selectivity profile, favoring EPHA4 over the other ephrin receptor kinase family members. The dual EPHA2/GAK inhibitor 55 prevented dengue virus infection of Huh7 liver cells, mainly via its EPHA2 activity, and is therefore a promising candidate for further optimization of its activity against dengue virus.

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Gerninghaus, J., Zhubi, R., Kraemer, A., Karim, M., Tran, D. H. N., Joerger, A. C., Schreiber, C., Berger, L. M., Berger, B. T., Ehret, T. A. L., Elson, L., Lenz, C., Saxena, K., Mueller, S., Einav, S., Knapp, S., Hanke, T.. 2024-02-18. Back-pocket optimization of 2-aminopyrimidine-based macrocycles leads to potent dual EPHA2/GAK kinase inhibitors with antiviral activity. https://doi.org/10.1101/2024.02.18.580805

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