Targeting the undruggables ---- the power of protein degraders

Undruggable targets typically refer to a class of therapeutic targets that are difficult to target through conventional methods or have not yet been targeted, but are of great clinical significance. Typical examples of undruggable targets include: 1) transcription factors, such as signal transducer and activator of transcription (STAT), myelocytomatosis oncogene (Myc) protein, and tumor protein 53 (p53). 2) GTPases, such as the rat sarcoma (RAS) family protein KRAS. 3) intrinsically disordered proteins, such as Tau protein. 4) protein-protein interactions, such as the anti-apoptotic B-cell lymphoma 2 (BCL2) protein family. 5) phosphatases, such as Src homology-2 domain-containing protein tyrosine phosphatase-2 (SHP2). According to statistics, over 80% of disease-related pathogenic proteins cannot be targeted by current conventional treatment methods.

In recent years, with the advancement of basic research and new technologies, the development of various new technologies and mechanisms has brought new perspectives to overcome challenging drug targets. Among them, targeted protein degradation technology is a breakthrough drug development strategy for challenging drug targets. This technology can specifically identify target proteins and directly degrade pathogenic target proteins by utilizing the inherent protein degradation pathways within cells. This new form of drug development includes various types such as PROteolysis TArgeting Chimera (PROTAC), molecular glue, LYsosome-TArgeting Chimaera (LYTAC), Autophagosome-TEthering Compound (ATTEC), AUtophagy-TArgeting Chimera (AUTAC), AUTOphagy-TArgeting Chimera (AUTOTAC), Degrader-Antibody Conjugate (DAC), etc. This article systematically summarizes the application of targeted protein degradation technology in the development of degraders for challenging drug targets.

PROTAC technology achieves targeted protein degradation by connecting ligands for target proteins and E3 ligases using chemical linkers. This connection recruits the E3 ligase to the vicinity of the target protein, utilizing the cellular ubiquitin-proteasome system to ubiquitinate and degrade the target protein. Molecular glues are small molecules that induce close proximity between two proteins, enabling precise temporal control over various biological processes, such as signal transduction, transcription, chromatin regulation, as well as protein folding, localization, and degradation. As proximity-inducing chemical inducers, molecular glues promote dimerization or co-localization of two proteins, resulting in diverse biological and pharmacological functions. Typically, molecular glues have small molecular weights and physicochemical properties that are easy to optimize. They primarily induce or stabilize protein-protein interactions between ubiquitin ligases and substrate proteins, leading to protein degradation. Molecular glues can degrade undruggable target proteins without the need for a binding pocket on the target protein.

In addition to PROTAC and molecular glue, other targeted protein degradation techniques have also found significant applications in the development of degraders for undruggable proteins.

Degrader-antibody conjugates (DACs) akin to traditional antibody-drug conjugates (ADCs) but replacing toxins with degraders like PROTAC or molecular glue, functions by antibody recognition of target antigens, followed by internalization and cleavage of the linker to release the degrader through enzymatic action. DAC presents potential advantages over PROTAC, including the ability to deliver degraders with poor drug metabolism and pharmacokinetics (DMPK) properties, enhance PROTAC exposure, and target specific tumors or tissues. However, DAC development is intricate, requiring degraders with targeted biological activity, high drug-to-antibody ratios potentially leading to aggregation issues, novel linker designs for larger or more lipophilic PROTAC molecules, and ensuring junctions between PROTAC and the linker do not interfere with biological functions, alongside considerations for degrader payload stability in lysosomal systems.

Similar to PROTACs, LYTACs are bifunctional molecules with two binding domains. One end carries a glycopeptide moiety that binds to the cell surface transmembrane receptor CI-M6PR (cation-independent mannose-6-phosphate receptor), and the other end carries an antibody or small molecule that binds to the target protein. AUTAC (Autophagy Targeting Chimera) technology is a novel approach that utilizes the cellular autophagic machinery to promote the degradation of specific proteins. Similar to PROTAC and LYTAC, AUTAC technology employs a chimera strategy designed to guide specific proteins into the autophagic pathway. AUTAC molecules consist of three components: a cGMP-based degradation tag, a linker, and a small molecule ligand for the protein of interest (POI) or organelle. AUTAC molecules trigger K63-linked polyubiquitination, followed by lysosome-mediated degradation.

The Autophagosome-Tethering Compound (ATTEC) is another technology developed for targeted protein degradation through the autophagy pathway. ATTEC utilizes autophagosomes to transport target proteins to lysosomes for degradation. It is based on the specific labeling of a protein on the surface of autophagosomes – Microtubule-associated protein 1A/1B-light chain 3 (LC3), to facilitate the transport and degradation of targeted proteins.

Autophagy-targeting chimeras (AUTOTACs) directly interact with the ZZ-type zinc finger (ZZ) domain of sequestosome 1 (SQSTM1)/p62 without the need for polyubiquitination. Specific autophagy-targeting ligands (ATLs) have been developed specifically for synthesizing AUTOTACs. The autophagic cargo receptor p62/SQSTM1 acts as a bridge between polyubiquitinated cargo and autophagosomes. Polyubiquitinated cargo binds to the UBA domain of p62, leading to a conformational change in p62. This conformational change exposes the LIR motif of p62, facilitating its interaction with LC3 on the autophagic membrane.

Finally, the article looks forward to the future development direction and application prospects of targeted protein degradation technology. Continuously optimizing existing degradation technologies and tackling even more challenging undruggable proteins will be critical directions for future breakthroughs. In addressing the aforementioned challenges, strategies for rapidly and efficiently constructing diverse molecular libraries, such as AI-assisted virtual drug screening technology and DNA-encoded library (DEL) screening technology, can be instrumental. These approaches can aid in the development of specific PROTACs, molecular glues, or other degraders tailored for undruggable targets.

As of now, more than 30 pipelines based on TPD technology are undergoing clinical trials, primarily in the field of oncology. Beyond cancer, many targeted protein degradation drugs show significant promise in treating neurodegenerative diseases, autoimmune diseases, inflammatory conditions, as well as viral and bacterial infections. Overall, the application prospects of targeted protein degradation technologies are undoubtedly promising. Leading institutes around the world are actively promoting molecular glue technology. Major global pharmaceutical companies are also actively involved in the research and development of protein degrader drugs. Currently, the two leading anti-tumor drugs in research are from a biotechnology company in the United States, and once approved, it will become the world's first PROTAC drug. Furthermore, in recent years, an increasing number of PROTAC degraders have begun entering clinical trials. These new targets of PROTACs include BCL-xL, IRAK4, STAT3, BTK, BRD9, MDM2, and others.

In comparison to these well-known treatment technologies, protein degradation and molecular glue technologies are more cutting-edge and innovative. Increasing investment in the original innovation development of key technologies will undoubtedly benefit the protein degradation and molecular glue pharmaceuticals.

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