Target‐Templated Construction of Functional Proteomimetics Using Photo‐Foldamer Libraries

• Published in: Angewandte Chemie 2025-01, Vol.137 (2), p.n/a
• Main Authors: Wéber, Edit, Ábrányi‐Balogh, Péter, Nagymihály, Bence, Menyhárd, Dóra K., Péczka, Nikolett, Gadanecz, Márton, Schlosser, Gitta, Orgován, Zoltán, Bogár, Ferenc, Bajusz, Dávid, Kecskeméti, Gábor, Szabó, Zoltán, Bartus, Éva, Tököli, Attila, Tóth, Gábor K., Szalai, Tibor V., Takács, Tamás, Araujo, Elvin, Buday, László, Perczel, András, Martinek, Tamás A., Keserű, György M.
• Format: Article
• Language: English
• Subjects: Affinity; Allosteric properties; Crosslinking; foldamer; fragment screening; Ligands; Peptide mapping; photoaffinity labeling; protein design; protein-protein interaction; Proteins; Stat3 protein; Structural analysis; Target detection
• ISSN: 0044-8249; 1521-3757
• DOI: 10.1002/ange.202410435

Current methods for proteomimetic engineering rely on structure‐based design. Here we describe a design strategy that allows the construction of proteomimetics against challenging targets without a priori characterization of the target surface. Our approach employs (i) a 100‐membered photoreactive foldamer library, the members of which act as local surface mimetics, and (ii) the subsequent affinity maturation of the primary hits using systems chemistry. Two surface‐oriented proteinogenic side chains drove the interactions between the short helical foldamer fragments and the proteins. Diazirine‐based photo‐crosslinking was applied to sensitively detect and localize binding even to shallow and dynamic patches on representatively difficult targets. Photo‐foldamers identified functionally relevant protein interfaces, allosteric and previously unexplored targetable regions on the surface of STAT3 and an oncogenic K‐Ras variant. Target‐templated dynamic linking of foldamer hits resulted in two orders of magnitude affinity improvement in a single step. The dimeric K‐Ras ligand mimicked protein‐like catalytic functions. The photo‐foldamer approach thus enables the highly efficient mapping of protein‐protein interaction sites and provides a viable starting point for proteomimetic ligand development without a priori structural hypotheses. Expedient generation of functional proteomimetics was achieved without relying on any a priori structural hypotheses concerning target binding. A 100‐membered photoreactive local surface mimetic foldamer library mapped the challenging protein targets, yielding the primary hits. From these building blocks, a dynamic covalent selection based affinity amplification was achieved by hit‐ligation.