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KianBV authored Oct 7, 2024
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Cells not only constantly produce proteins, but also continuously break down old, damaged, or unnecessary ones. This protein degradation process is vital for maintaining cellular health and is often centred around ubiquitination—a system where unwanted proteins are tagged with a small molecule called ubiquitin. The presence of ubiquitin signals to the cell’s "garbage disposal" system, the ubiquitin-proteasome system (UPS), to degrade these proteins[^ubi_first].

The UPS involves several important steps and enzymes to ensure that only the right proteins are marked for destruction. Here, three enzymes are involved in the tagging process: Ubiquitin-activating enzymes (E1), ubiquitin-conjugating enzymes (E2), and E3 ligases. In humans, the UBA1 enzyme (E1) usually starts the process by attaching ubiquitin to one of about 40 E2 enzymes. The E3 ligase then plays a critical role, acting as a "scout" that identifies which protein needs to be degraded by recognizing different signals, such as specific peptide sequences called degrons, on the target protein. The E3 ligase attaches the first ubiquitin molecule, initiating the formation of a polyubiquitin chain, which can mark the protein for breakdown in the proteasome[^ubi_second]. Here, proteins are broken down into smaller pieces for reuse or disposal [^ubi_third][^ubi_fourth].
The UPS involves several important steps and enzymes to ensure that only the right proteins are marked for destruction. Here, three enzymes are involved in the tagging process: Ubiquitin-activating enzymes (E1), ubiquitin-conjugating enzymes (E2), and E3 ligases. In humans, the UBA1 enzyme (E1) usually starts the process by attaching ubiquitin to one of about 40 E2 enzymes. The E3 ligase then plays a critical role, acting as a "scout" that identifies which protein needs to be degraded by recognizing different signals, such as specific peptide sequences called degrons, on the target protein. After recognition the first ubiquitin molecule is attached to the target, initiating the formation of a polyubiquitin chain. This can mark the protein for degradation in the proteasome[^ubi_second], where proteins are broken down into smaller pieces for reuse or disposal [^ubi_third][^ubi_fourth].

The UPS is highly selective, ensuring that only the right proteins are degraded. However, sometimes this system fails to properly address problematic proteins, which can lead to diseases, such as cancer or autoimmune diseases [^ubi_fifth][^ubi_sixth]. To overcome this, researchers have turned to Targeted Protein Degradation (TPD), a cutting-edge therapeutic approach that directs the body’s own degradation machinery toward disease-causing proteins. Current TPD strategies include small molecules like PROTACs (proteolysis-targeting chimeras) and molecular glues, which help guide harmful proteins to be tagged with ubiquitin and destroyed by the UPS [^ubi_first].
The UPS is highly selective, ensuring that only the right proteins are degraded. However, sometimes this system fails to properly address problematic proteins, which can lead to diseases, such as cancer or autoimmune diseases [^ubi_fifth][^ubi_sixth]. To overcome this, researchers have turned to Targeted Protein Degradation (TPD), a cutting-edge therapeutic approach that directs the body’s own degradation machinery toward disease-causing proteins. Current TPD strategies include small molecules like PROTACs (proteolysis-targeting chimeras) and molecular glues, which help guide harmful proteins to be tagged with ubiquitin and destroyed by the UPS [^ubi_first].

Despite their promise, current TPD methods face significant challenges. They can mistakenly tag healthy proteins for degradation, leading to unwanted off-target effects. Furthermore, these approaches may be inherently toxic or suffer from poor pharmacokinetic properties, complicating their development into safe and effective treatments (**10.1038/s41573-021-00371-6**). These limitations underscore the need for novel advancements to improve the precision of targeting harmful proteins, which could greatly enhance both the effectiveness and safety of protein degradation therapies.

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