Proteolysis Targeting Chimeras (PROTACs) have fundamentally transformed our approach to targeted therapeutics, offering a paradigm shift from traditional protein inhibition to selective protein degradation. These hetero-bifunctional molecules hijack the ubiquitin proteasome system to selectively add polyubiquitin chains onto a specific protein target to induce proteolytic degradation, enabling researchers to target previously “undruggable” proteins that lack suitable binding pockets for small-molecule inhibitors. As we advance into 2025 and beyond, PROTAC technology stands at a critical juncture where foundational successes are paving the way for next-generation innovations that promise to address current limitations and expand therapeutic applications across diverse disease areas.
Expanding the E3 Ligase Toolkit
One of the most significant limitations in current PROTAC development lies in the restricted repertoire of E3 ligases utilized for protein degradation. However, only thirteen of the ∼600 E3s have been employed in PROTAC designs, namely Arylhydrocarbon Receptor (AhR), Cereblon (CRBN), Cellular Inhibitor of Apoptosis 1 (cIAP1), DDB1 And CUL4 Associated Factor 11 (DCAF11), DCAF15, DCAF16, Fem-1 Homolog B (FEM1B), Kelch-like ECH-associated Protein 1 (KEAP1), Mouse Double Minute 2 Homolog (MDM2), Ring Finger Protein 4 (RNF4), RNF114, Von Hippel-Lindau Tumor Suppressor (VHL), and X-linked IAP (XIAP). This represents an enormous untapped potential, with approximately 98% of human E3 ligases remaining unexplored for PROTAC applications. The identification and characterization of novel E3 ligases will be crucial for expanding target coverage, improving tissue-specific degradation, and overcoming resistance mechanisms. Recent advances in mass spectrometry-based approaches for E3 ligase discovery and validation are beginning to address this challenge, with emerging platforms enabling systematic screening of E3-target interactions.
Overcoming Physicochemical Challenges
Traditional PROTACs face significant challenges related to their molecular properties, particularly high molecular weight (0.6–1.3 kDa) relative to classical small molecule inhibitors (<0.5 kDa) and large polar surfaces of PROTACs remain a challenge in designing new PROTACs, as these biophysical characteristics restrict their solubility and permeability, and consequently reduce their bioavailability for clinical use and oral administration. The field is responding with innovative approaches including peptide PROTACs, which leverage the natural degradation machinery while offering advantages in terms of target specificity and reduced toxicity. Compared with small-molecule PROTACs, peptide PROTACs have advantages such as multitargeting, biodegradability, low toxicity, and flexibility in structural design. Additionally, advanced delivery systems including nano-PROTACs and biomacromolecule-PROTAC conjugates are being developed to improve tissue targeting and overcome permeability barriers.
Clinical Translation and Advanced PROTAC Modalities
The clinical landscape for PROTACs is rapidly evolving, with the third PROTAC molecule worldwide reaching Phase III stage representing significant progress in translating this technology to patients. Vepdegestrant (ARV-471) is the world’s first oral PROTAC molecule to advance into Phase III clinical trials, while BMS-986365 is a potent ligand-directed degrader (LDD) that promotes CRL4^CRBN E3 ubiquitin ligase–dependent ubiquitination and degradation of the androgen receptor (AR). Beyond these pioneering molecules, the field is witnessing the emergence of sophisticated PROTAC modalities including conditional degraders, light-activated PROTACs, and tissue-specific delivery systems that promise enhanced therapeutic windows and reduced off-target effects.
Addressing Resistance and Selectivity Challenges
As PROTAC technology matures, understanding and overcoming resistance mechanisms becomes increasingly critical. Despite recent attempts to advance the clinical application of second-generation PROTACs, the majority of these compounds fail to progress beyond the preclinical stage in drug development. One of the most formidable challenges lies in achieving precise protein degradation of desired targets. The development of combination strategies, next-generation PROTACs with improved selectivity profiles, and approaches to monitor and counteract resistance will be essential for long-term clinical success. Advanced proteomics approaches are proving invaluable for understanding these mechanisms and guiding rational design strategies.
The Transformative Impact of Proteomics and Metabolomics
The integration of proteomics, phosphoproteomics, and metabolomics represents a paradigm shift in PROTAC research and development, offering unprecedented insights into degrader mechanisms, selectivity, and efficacy. Contract Research Organizations (CROs) like Panome Bio are at the forefront of delivering these multi-omics solutions to advance PROTAC development. Mass spectrometry-based proteomics profiling enables researchers to comprehensively map PROTAC-induced changes across the cellular proteome, revealing direct target degradation events while simultaneously identifying off-target effects and downstream pathway modulation. Phosphoproteomics adds a critical dimension by capturing the dynamic changes in protein phosphorylation states that occur following target protein degradation, providing insights into signaling pathway perturbations and kinase cascade alterations that may contribute to therapeutic efficacy or resistance mechanisms. These post-translational modification analyses are particularly valuable for understanding how PROTAC-mediated degradation affects cellular signaling networks and can inform the design of more selective degraders. Metabolomics complements these protein-level analyses by providing a functional readout of PROTAC activity at the metabolic level, capturing the downstream consequences of protein degradation on cellular metabolism, energy production, and biosynthetic pathways. This integrated multi-omics approach enables researchers to develop comprehensive mechanistic models of PROTAC action, identify predictive biomarkers for clinical response, and optimize degrader selectivity and efficacy through data-driven design strategies that account for the complex interplay between protein degradation, signaling networks, and metabolic reprogramming.