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Targeted protein degradation is a promising approach for developing new drugs, especially for diseases caused by proteins that are difficult to inhibit using traditional small molecule inhibitors. By understanding the phenotypic consequences of degrading a specific protein, researchers can assess the potential therapeutic benefits and risks of using protein degradation as a treatment strategy. 

Here we describe a fast and efficient way to characterize protein degradation phenotype using HaloPROTAC3. 

Learn About HaloPROTAC3

What Is the Phenotypic Consequence of Target Degradation? 

Temporal degradation of proteins inside a cell often elicits a much different phenotype than genetic knockouts or protein mutations. HaloPROTAC3, a fusion of a HaloTag® label and a PROTAC, is a rapid and highly effective way to understand and characterize protein degradation phenotype.

HaloPROTAC3 recruits an endogenous VHL E3 ligase component to a HaloTag® fusion protein, resulting in ubiquitination and degradation via the proteasome pathway. HaloPROTAC3 contains a degradation-inducing acylamine moiety, coupled to a chloroalkane moiety by a linker of variable length.

To study endogenous protein loss in relevant cell backgrounds, we recommend incorporating a tag into the target protein loci via CRISPR/Cas9 gene editing. Loss of protein is monitored in cells treated with HaloPROTAC3 using live-cell luminescence. HaloPROTAC3 shows fast burst loss that is sustained over time with endogenously tagged HaloTag® fusion proteins.

HaloPROTAC overview

Schematic overview of HaloPROTAC function.

BRD4 degradogram

The HiBiT-BRD4 degradogram. BRD4, endogenously tagged with HiBiT and HaloTag® label, is degraded using increasing concentrations of HaloPROTAC and quantified using  HiBiT luminescence.


HaloPROTAC3 degradation of HiBiT-HaloTag CRISPR targets in various compartments. Results show rapid, burst degradation of targets in multiple cellular compartments, including single-pass mitochondrial membrane protein, with HaloPROTAC3. This confirms the proteins can be targeted via proteasomal degradation strategies.

Ready to start your degradation assays with HaloPROTAC3?
 View HaloPROTAC Ligands

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