Synthesis of Self-Assembling Proteolysis Targeting Chimeras Based on Biorthogonal Reactions

Proteolysis targeting chimeras (PROTACs) are heterobifunctional molecules composed of a ligand of a protein of interest (POI) and a ligand for an E3 ligase, connected by a linker, capable of inducing ubiquitination and proteasomal degradation of the POI; however, their size and physicochemical properties often violate Lipinski’s rule of five, potentially leading to bioavailability issues[1]. A promising alternative is represented by in-cell self-assembling PROTACs, in which the degrader is split into two fragments bearing biorthogonal groups that react intracellularly to generate the active molecule. In this work, potential self-assembling PROTACs targeting BRD4, an epigenetic reader involved in oncogenic transcription, were synthetized. The BRD4 inhibitor (+)-JQ1 3 was functionalized with a terminal vinyl boronic acid (VBA), while the CRBN recruiter lenalidomide was functionalized with a tetrazine moiety (Tz). Molecular docking studies, based on available crystal structures of both proteins in complex with their respective ligands, guided linker design, while molecular dynamics simulations supported the stability of both binary (PROTAC–BRD4 and PROTAC–CRBN) and ternary (BRD4–PROTAC–CRBN) complexes. Ongoing studies include biophysical evaluation of binding affinities, assessment of intracellular assembly, and analysis of degradation activity through cellular assays. References: [1] He, S. et al.; Med. Res. Rev., 2022, 42 (3), 1280–1342. https://doi.org/10.1002/med.21877. [2] Eising, S. et al.; Bioconjug. Chem., 2018, 29 (4), 982–986. https://doi.org/10.1021/acs.bioconjchem.7b00796. [3] Filippakopoulos, P. et al.; Nature, 2010, 468 (7327), 1067–1073. https://doi.org/10.1038/nature09504. [4] Guo, Z. et al.; J. Med. Chem., 2022, 65 (9), 6573–6592. https://doi.org/10.1021/acs.jmedchem.1c01876.