A Systematic Approach to the Discovery of Protein-Protein Inter-action Stabilizers

Kenanova, D. N.; Visser, E. J.; Virta, J. M.; Sijbesma, E.; Centorrino, F.; Vickery, H. R.; Zhong, M.; Neitz, J. R.; Brunsveld, L.; Ottmann, C.; Arkin, M. R.

doi:10.1101/2023.01.29.526112

bioRxiv · 10.1101/2023.01.29.526112

A Systematic Approach to the Discovery of Protein-Protein Inter-action Stabilizers

Kenanova, D. N.·Visser, E. J.·Virta, J. M.·Sijbesma, E.·Centorrino, F.·Vickery, H. R.·Zhong, M.·Neitz, J. R.·Brunsveld, L.·Ottmann, C.·Arkin, M. R.

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Abstract

Protein-protein interactions (PPIs) are responsible for the proper function of biological processes and, when dysregulated, commonly lead to disease. PPI stabilization has only recently been systematically explored for drug discovery despite being a powerful approach to selectively target intrinsically disordered proteins and hub proteins, like 14-3-3, with multiple interaction partners. Disulfide tethering is a site-directed fragment-based drug discovery (FBDD) methodology for screening small molecules in a quantitative, high-throughput manner. We explore the scope of the disulfide tethering technology for the discovery of selective fragments as starting points for the development of potent small molecule PPI stabilizers and molecular glues using the hub protein 14-3-3{sigma}. The complexes with 5 biologically and structurally diverse phospho-peptides, derived from the 14-3-3 client proteins ER, FOXO1, C-RAF, USP8, and SOS1, were screened for hit identification. Stabilizing fragments could be found for 4/5 client complexes with a diversified hit-rate and stabilizing efficacy for the different 14-3-3/client phospho-peptides. Extensive structural elucidation revealed the ability and adaptivity of the peptide to make productive interactions with the tethered fragments as key criterion for cooperative complex formation. We validated eight fragment stabilizers, six of which showed selectivity for one phospho-peptide client, and structurally characterized two nonselective hits and four fragments that selectively stabilized C-RAF or FOXO1. The most efficacious of these fragments increased 14-3-3{sigma}/C-RAF phospho-peptide affinity by 430-fold. Disulfide tethering to the wildtype C38 in 14-3-3{sigma} provided diverse structures for future optimization of 14-3-3/client stabilizers and highlighted a systematic method to discover molecular glues.

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Kenanova, D. N., Visser, E. J., Virta, J. M., Sijbesma, E., Centorrino, F., Vickery, H. R., Zhong, M., Neitz, J. R., Brunsveld, L., Ottmann, C., Arkin, M. R.. 2023-01-30. A Systematic Approach to the Discovery of Protein-Protein Inter-action Stabilizers. https://doi.org/10.1101/2023.01.29.526112

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