Freie Universität Berlin, Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Königin-Luise-Str. 2+4, 14195 Berlin, Germany.
Fragment-based drug discovery has been established as a powerful method for the assembly of optimized protein ligands. We have employed protein-templated ligations for the site-directed detection of low-affinity fragments and subsequently for the identification of potent fragment combinations useful as chemical tools.[1-5]
Reversible and irreversible reactions have been employed for ligand construction. Here, I will reflect on the reaction scope of protein-catalyzed ligand formation and consider the thermodynamic and kinetic implications of the reactions. Our results suggest that single interactions like H-bonds between the target protein and its ligand are sufficient to induce chemical reactivity which evolves potent and specific bioactive molecules from inactive precursors.
The approach will be demonstrated for the chemical evolution of viral protease inhibitors. Orthosteric inhibitors of the oncogenic protein tyrosine phosphatase SHP2 have been provided and validated in cells and animal models as potent anti-cancer agents.
Finally, I will show that the oncogenic transcription factor STAT5 is able to catalyze Mannich ligation reactions of fragments yielding inhibitors of leukemic cell proliferation. pH-dependency and protein-specificity of the protein-induced multicomponent reaction are studied and the ligands formed are validated in biophysical and biological studies. Best inhibitors of STAT5´s protein-protein interactions disrupt ternary STAT5-DNA complexes, block phosphorylation of STAT5, gene transcription by STAT5 and induce apoptosis specifically in STAT5-dependent leukemic cells in mice.
1. Schmidt, M. et al. Sensitized detection of inhibitory fragments and iterative development of non-peptidic protease inhibitors by Dynamic Ligation Screening, Angew. Chem. Int. Ed. 2008, 47, 3275.
2. Becker, D. et al. Irreversible inhibitors of the 3C protease of Coxsackie virus through templated assembly of protein-binding fragments, Nature Commun. 2016, 7, 12761.
3. Jaegle, M. et al. Protein-templated formation of an inhibitor of the blood coagulation factor Xa through a background-free amidation reaction, Angew. Chem. Int. Ed. 2017, 56, 3718.
4. Jaegle, M. et al. Protein-templated fragment ligations: from molecular recognition to drug discovery, Angew. Chem. Int. Ed. 2017, 56, 7358.
5. Wong, E. L. et al. The transcription factor STAT5 catalyzes Mannich ligation reactions yielding inhibitors of leukemic cell proliferation. Nature Commun. 2019, 10, 66.