RuPHOTACs provide photocontrol over protein degradation with optimized properties for biological applications

PROteolysis TArgeting Chimeras (PROTACs) are bifunctional molecules that catalyze degradation of selected proteins by inducing protein:protein interactions (PPIs) between E3 ubiquitin ligases and the protein of interest. A critical limitation is undesired effects in untargeted tissues, necessitating approaches to impose spatiotemporal control over PROTAC function. Here we present Ru(II) photocages that can be released with low energy light, providing triggered PROTAC activity on demand. The systems, termed Ruthenium-based PHOToActivated Chimeras (RuPHOTACs), were validated by targeting bromodomain-containing proteins, which act as crucial epigenetic regulators, and also strongly reduced levels of c-MYC and PIM1. RuPHOTACs demonstrate that the incorporation of metal components within organic PROTACs confers multiple advantages for light-controlled systems for chemical biology applications, including the highest selectivity for activation in the light vs. the dark, improved potency against the target proteins of interest, and increased efficacy in vivo using low energy red light. To efficiently monitor protein degradation via optical means, a strategy was implemented by creating a fusion of a photoconvertible protein, Dendra2, with the proteins of interest. This bifunctional reporter system for live cell analysis decouples protein degradation efficiency and rates from signals arising from new protein production, and is superior to prior reporter systems described for PROTACs because it directly measures the true degradation rate of the target protein in intact, viable cells while simultaneously tracking newly synthesized protein without perturbing translation, proteostasis, or cell health. PROTACs offer a powerful strategy to eliminate disease-relevant proteins, but off-target activity in healthy tissues remains a major challenge. Here, the authors introduce Ruthenium-based PHOToActivated Chimeras (RuPHOTACs), a new class of light-responsive PROTACs that remain inactive until triggered by low-energy light.