PROTACs - Towards Revolutionizing Medicine and Therapies

PROTAC stands for proteolysis-targeting chimeras. These multifunctional units are designed to specifically target mutated enzymes or other proteins, used for proteasomal degradation. PROTAC molecules consist of a protein-binding site, a ligand, and a linker molecule or ion. PROTAC target and label target proteins with ubiquitin flags for proteasome-based degradation. The historical development started from almost 2001, wherein the advent of PROTAC molecules was conceptualized by Craig Crews and Raymond Deshaies, and they synthesized PROTAC-1 that targeted enzyme Methionine aminopeptidase-2 for catalytic degradation. Compared to traditional inhibitors, PROTACs display multiple benefits that make their desirable usage as drugs. Some PROTACs have been shown to be beneficial as compared to their inhibitor analogues. This also helps prevent mutation-driven drug resistance, often found with enzymatic inhibitors.

Mechanism of Action

PROTACs are composed of three parts – a ligand at one end that specifically binds to targeted protein molecule (POI), a linker that ligates ligand to the E3 ligase ligand, and an E3 ligase ligand that recruits E3 ubiquitin ligase molecules to the site of action. When the ‘ligand’ part binds to targeted ‘undruggable’ protein molecule, they form a stable complex. The ‘E3 ligand’ part of PROTAC binds to ‘E3 ubiquitin ligase’ to recruit more ubiquitin molecules into the system. This binding activates the ubiquitin-dependent proteasomal degradation cascade. Targeted proteins get in close proximity to E3 ligase, forming a ternary complex.

Next step is of ubiquitination, wherein ubiquitin molecules transfer away from ‘E3 ligase’ and catalytically attach to the targeted protein molecules, ‘red-flagging’ them for proteasomal breakdown. This process is catalyzed by enzyme E3 ligase. Ubiquitin ‘flagged’ targeted proteins are surrounded by proteasomal complex, leading to their hydrolytic breakdown into smaller peptides. This way, the target proteins get degraded, to render sustained therapeutic action in case of various cardiovascular, hepatic, endocrinal, respiratory, oncogenic, hematological, bone-related, neurological, ophthalmic diseases, etc.

Applications

1. Targeting of oncogenes – PROTAC molecules target and degrade apoptotic proteins that may trigger cancer cell proliferation.
2. Bypassing drug resistance mechanisms – They may target proteins involved in antibiotic drug resistance mechanisms. PROTACs target the entire protein/enzyme, irrespective of the condition where the binding site of the enzyme is mutated.
3. PROTACs can be designed to target mutated/overexpressed cancer subtypes. They may also target cancer stem cells in individuals predisposed to familial cancers.
4. Inflammatory cells – PROTACs may target proteins involved in the pathogenesis of autoimmune disorders and inflammatory responses by interfering with the synthesis of proteins involved in the synthesis and signalling of cytokines.
5. PROTACs may target proteins involved in the formation of amyloidal plaques, neurofibrillary tangles, and Lewy bodies, as seen in Alzheimer’s disease and Parkinson’s disease respectively.
6. Cardiovascular disorders – PROTACs can degrade proteins causing atherosclerotic plaques, cholesterol lipid depositions in blood vessels, and blood clots.
7. PROTACs may target viral proteins involved in viral replication, entry, spread, assembly, and proliferation within host cells.
8. PROTACs can be extended to agriculture and horticulture, where they may be used to develop novel pest-resistant varieties and control measures.
9. PROTACs may be tailored according to one’s genotypic composition, thereby standing out as a potential tool in personalized medicine.
10. PROTACs may target proteins involved in relieving chronic pain by interfering with the pain signalling pathways.
11. PROTACs may interfere with the neurotransmission of impulses, offering novel treatments for psychiatric disorders like depression and schizophrenia.
12. PROTACs may target any specific mutated hormone/enzyme involved in metabolic pathways, which lead to the development of various cardiovascular, hepatic, endocrinal, respiratory, oncogenic, hematological, bone-related, neurological, ophthalmic diseases, etc.

Future Prospects

PROTAC technology opens gates to novel prospects of treatment in the field of neurodegenerative disorders. PROTACs can target proteins or mutated proteins that have complex structures. These proteins or drugs are required in minimal doses with the least side effects. However, the high molecular weight of such proteins that hampers cell permeability, off-targeting effects, cytotoxicity instances, and pharmacokinetics needs to be worked out still. This technology can also be unified with personalized medicine. Ongoing research aims to enhance the versatility of PROTAC molecules and overcome the aforementioned challenges.

References

1. Tejwani, V., Carroll, T., Macartney, T., Bandau, S., Alabert, C., Saredi, G., & Rouse, J. (2024). PROTAC-mediated conditional degradation of the WRN helicase as a potential strategy for selective killing of cancer cells with microsatellite instability. Scientific Reports, 14(1), 20824.
2. Pedrucci, F., Pappalardo, C., Marzaro, G., Ferri, N., Ferlin, A., & De Toni, L. (2022). Proteolysis targeting chimeric molecules: Tuning molecular strategies for a clinically sound listening. International Journal of Molecular Sciences, 23(12), 6630.
3. Zhao, L., Zhao, J., Zhong, K., Tong, A., & Jia, D. (2022). Targeted protein degradation: mechanisms, strategies and application. Signal Transduction and Targeted Therapy, 7(1), 113.
4. Arduengo, M. (2022, March 7). Using structural computation models to predict productive PROTAC ternary complexes. Promega Connections. https://www.promegaconnections.com/protac-ternary-complex
5. Biolabs. (2021, March 24). Pros and Cons of PROTAC Technology – Creative Biolabs PROTAC Blog. https://www.creative-biolabs.com/blog/protac/protac-reviews/pros-and-cons-of-protac-technology
6. Cecchini, C., Pannilunghi, S., Tardy, S., & Scapozza, L. (2021). From conception to development: investigating PROTACs features for improved cell permeability and successful protein degradation. Frontiers in Chemistry, 9, 672267.
7. Schade, M., Scott, J. S., Hayhow, T. G., Pike, A., Terstiege, I, Ahlqvist, M.,  & Wilson, D. (2024) Structural and physicochemical features of oral PROTACs. Journal of Medicinal Chemistry, 67(15), 13106–13116.

Authors

Mr. Avanish Prakash¹ and Dr. Ashwini Puntambekar²

¹M.Sc. Biotechnology second year student

²Assistant Professor, Protein Biochemistry Research Center,

Dr. D. Y. Patil Biotechnology and Bioinformatics Institute,

Dr. D. Y. Patil Vidyapeeth, Pune - 411033, Maharashtra, India.