Branching beyond bifunctional linkers: synthesis of macrocyclic and trivalent PROTACs

Proteolysis-targeting chimeras (PROTACs) are traditionally conceptualized and synthesized by connecting two ligands, one for a target protein and one for an E3 ligase, via a bifunctional linker. Chemical creativity has recently explored the development of more elaborate and unusual linkers beyond conventional bifunctionals, allowing the development of macrocyclic and trivalent PROTACs. In two distinct proof-of-concept studies guided by the co-crystal structure of bivalent PROTAC MZ1 in complex with the E3 ubiquitin ligase von Hippel-Lindau and the second bromodomain of Brd4, we designed macrocyclic macroPROTAC-1 and trivalent PROTAC SIM1. These designs aimed to enhance protein degradation by constraining the PROTAC in its bioactive conformation or increasing avidity and cooperativity within the PROTAC ternary complex by augmenting the binding valency to the target protein, respectively. Here we describe the step-by-step synthesis of the macrocyclic macroPROTAC-1 and trivalent PROTAC SIM1, detailing the generation of the macrocyclic and trivalent cores and their subsequent conjugation to the respective ligands. This two-part procedure is expected to take ~14 d for the synthesis of macroPROTAC-1 and 10 d for the synthesis of SIM1. In this protocol, we also provide a brief introduction into the biophysical and cellular evaluation of these unusual molecules, representative structures of key negative control compounds and their utility, and highlight recent developments and expansion beyond pioneering exemplars.