BPI Technology Advances Targeted Protein Degradation — A Site-Specific Strategy to Accelerate Drug Discovery

Introduction

Targeted protein degradation (TPD) has emerged as a transformative strategy in drug discovery, offering a means to eliminate disease-relevant proteins rather than simply inhibiting them. A recent publication in Cell Chemical Biology (July 17, 2025) introduces a powerful platform that may overcome key limitations of TPD. This innovation, called BPI (Bioorthogonal Proximity Inducer) technology, allows researchers to evaluate proximity-induced degradation at the resolution of individual amino acid residues — without requiring dedicated ligands for each protein site.

What is Targeted Protein Degradation (TPD)?

TPD strategies such as PROTACs and molecular glues exploit the cell’s own ubiquitin-proteasome system to eliminate specific proteins. These agents typically link a ligand for a target protein to an E3 ubiquitin ligase, forming a ternary complex that enables selective ubiquitination and degradation.

However, TPD development has faced several barriers. Most clinical candidates rely on just a few E3 ligases like VHL or CRBN, and it remains difficult to assess which binding sites on an effector protein are optimal for degradation. Site dependence and ternary complex geometry play critical roles — but evaluating them requires developing specific ligands for each site, which is resource intensive.

What Is BPI Technology?

The BPI platform overcomes this bottleneck by combining genetic code expansion and ultrafast bioorthogonal chemistry. Specific unnatural amino acids (UAAs), such as BCNK, are incorporated into selected sites within E3 ligases (VHL, CRBN) or E2 enzymes (UBE2D1) in live cells. These UAAs allow covalent binding of a synthetic BPI probe carrying a known ligand (e.g., JQ1 targeting BET proteins) and a reactive group.

This strategy enables site-specific conjugation of a proximity-inducing probe to an effector protein — without needing to develop site-specific ligands. The result: a systematic, high-resolution evaluation of which sites are productive for inducing protein degradation.

Key Results: Degradation via VHL, CRBN, and UBE2D1

The authors demonstrated the power of the BPI system by evaluating degradation of BET family proteins (BRD2/3/4) using genetically sensitized variants of VHL, CRBN, and UBE2D1:

• VHL: When BCNK was incorporated at Asn67, the BPI probe induced robust degradation of BRD4 (D_max: 69%, DC₅₀: ~1 nM), rivaling or exceeding traditional PROTAC performance.
• CRBN: BCNK incorporation at Glu377 or His353 enabled degradation of BRD4 with a DC₅₀ of ~50 nM. CRBN showed broader site flexibility compared to VHL.
• UBE2D1: Surprisingly, E3-independent degradation was achieved using an E2 enzyme. Degradation varied by site, but monoubiquitination and lysosomal routing were observed — revealing non-proteasomal mechanisms.

All outcomes were quantified using HiBiT-tagged cell lines and luminescence assays. Control conditions confirmed proteasome dependence, cullin ligase activation requirements, and the hook effect at high BPI concentrations.

Implications for Drug Discovery

This site-resolved approach has several important implications:

• Accelerates degrader development by identifying optimal exit vectors and recruitment geometries
• Enables systematic evaluation of underused E3 ligases and E2 enzymes
• Facilitates development of tissue- or disease-specific degraders by screening effectors with restricted expression
• Supports applications in DNA-encoded library (DEL) screening and design of covalent degraders

Crucially, it also provides a practical method to evaluate whether a given protein is “degradable” — a longstanding question in TPD development.

Limitations and Future Outlook

As the system relies on genetic code expansion, its current use is limited to transfectable cell lines like HEK293. Expanding BPI into stable cell lines or in vivo models will be essential for translational use. Moreover, while the current BPI probes rely on JQ1 for BET targeting, the modular design could accommodate diverse ligands for other targets — making the platform adaptable across therapeutic areas.

Another exciting avenue lies in exploring unligandable proteins by tethering tags such as dTAG or BromoTag and screening proximity effects. Although the authors acknowledge some off-target amber suppression, their controls confirm degradation outcomes are effector-dependent and site-specific.

Author’s Perspective

The BPI platform represents a shift in how we approach TPD design. Rather than starting with ligand discovery, this method enables researchers to assess functional degrader geometry before investing in ligand optimization. In that sense, BPI can serve as a “pre-screening” or “pre-validation” tool to guide rational degrader development.

From a practical standpoint, the ability to identify which binding site delivers the most efficient degradation — even for non-E3 effectors — has enormous potential to unlock new targets, accelerate candidate triage, and ultimately bring new therapeutics to patients faster.

Reference: Cell Chemical Biology July 2005, Site-resolved assessment of targeted protein degradation