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Proteolysis targeting chimera

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TL 12-186, a thalidomide-based PROTAC targeting the protein GSPT1, a translation termination factor[1]

A proteolysis targeting chimera (PROTAC)[2] is a molecule that can remove specific unwanted proteins. Rather than acting as a conventional enzyme inhibitor, a PROTAC works by inducing selective intracellular proteolysis. A heterobifunctional molecule with two active domains and a linker, PROTACs consist of two covalently linked protein-binding molecules: one capable of engaging an E3 ubiquitin ligase, and another that binds to a target protein meant for degradation. Recruitment of the E3 ligase to the target protein results in ubiquitination and subsequent degradation of the target protein via the proteasome. Because PROTACs need only to bind their targets with high selectivity (rather than inhibit the target protein's enzymatic activity), there are currently many efforts to retool previously ineffective inhibitor molecules as PROTACs for next-generation drugs.[3][4]

Initially described by Kathleen Sakamoto, Craig Crews and Ray Deshaies in 2001,[5] the PROTAC technology has been applied by a number of drug discovery labs using various E3 ligases,[6] including pVHL,[7][8][9] CRBN,[10][11] Mdm2,[12] beta-TrCP1,[5] DCAF11,[13][14] DCAF15,[15] DCAF16,[15] RNF114,[15] and c-IAP1.[16] Yale University licensed the PROTAC technology to Arvinas in 2013–14.[17][18]

In 2019, Arvinas put two PROTACs into clinical trials: bavdegalutamide (ARV-110), an androgen receptor degrader, and vepdegestrant (ARV-471), an estrogen receptor degrader.[19][20] In 2021, Arvinas put a second androgen receptor PROTAC, Luxdegalutamide (ARV-766), into the clinic.[21]

Mechanism of action

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Mechanism. E1, E2, E3: ubiquitination enzymes; Ub = ubiquitin; target = protein to be degraded[1]

PROTACs achieve degradation through "hijacking" the cell's ubiquitin–proteasome system (UPS) by bringing together the target protein and an E3 ligase.[22]

First, the E1 activates and conjugates the ubiquitin to the E2.[15] The E2 then forms a complex with the E3 ligase. The E3 ligase targets proteins and covalently attaches the ubiquitin to the protein of interest.[22] Eventually, after a ubiquitin chain is formed, the protein is recognized and degraded by the 26S proteasome.[19] PROTACs take advantage of this cellular system by putting the protein of interest in close proximity to the E3 ligase to catalyze degradation.[19]

Unlike traditional inhibitors, PROTACs have a catalytic mechanism, with the PROTAC itself being recycled after the target protein is degraded.[19]

Design and development

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The protein targeting warhead, E3 ligase, and linker must all be considered for PROTAC development. Formation of a ternary complex between the protein of interest, PROTAC, and E3 ligase may be evaluated to characterize PROTAC activity because it often leads to ubiquitination and subsequent degradation of the targeted protein.[15] A hook effect is commonly observed with high concentrations of PROTACs due to the bifunctional nature of the degrader.[15]

Currently, pVHL and CRBN have been used in preclinical trials as E3 ligases.[15] However, there still remains hundreds of E3 ligases to be explored, with some giving the opportunity for cell specificity.

Benefits

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Compared to traditional inhibitors, PROTACs display multiple benefits that make them desirable drug candidates. Due to their catalytic mechanism, PROTACs can be administered at lower doses compared to their inhibitor analogues,[20] though care needs to be taken in achieving oral bioavailability if administered by that route.[23] Some PROTACs have been shown to be more selective than their inhibitor analogues, reducing off-target effects.[20] PROTACs have the ability to target previously undruggable proteins, as they do not need to target catalytic pockets.[20] This also helps prevent mutation-driven drug resistance often found with enzymatic inhibitors.

PROTAC databases

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  • PROTACpedia, a manually curated and user-contributed PROTAC-specific public access database.
  • E3 Atlas, a comprehensive E3 database that characterizes the potential for specific E3 ligases to be employed for PROTAC design.[25]

References

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  1. ^ a b Ishoey M, Chorn S, Singh N, Jaeger MG, Brand M, Paulk J, et al. (March 2018). "Translation Termination Factor GSPT1 Is a Phenotypically Relevant Off-Target of Heterobifunctional Phthalimide Degraders". ACS Chemical Biology. 13 (3): 553–560. doi:10.1021/acschembio.7b00969. PMID 29356495.
  2. ^ Luh LM, Scheib U, Juenemann K, Wortmann L, Brands M, Cromm PM (September 2020). "Prey for the Proteasome: Targeted Protein Degradation-A Medicinal Chemist's Perspective". Angewandte Chemie. 59 (36): 15448–15466. doi:10.1002/anie.202004310. PMC 7496094. PMID 32428344.
  3. ^ Cermakova K, Hodges HC (August 2018). "Next-Generation Drugs and Probes for Chromatin Biology: From Targeted Protein Degradation to Phase Separation". Molecules. 23 (8): 1958. doi:10.3390/molecules23081958. PMC 6102721. PMID 30082609.
  4. ^ Noblejas-López MD, Tébar-García D, López-Rosa R, Alcaraz-Sanabria A, Cristóbal-Cueto P, Pinedo-Serrano A, et al. (October 2023). "TACkling Cancer by Targeting Selective Protein Degradation". Pharmaceutics. 15 (10): 2442. doi:10.3390/pharmaceutics15102442. PMC 10610449. PMID 37896202.
  5. ^ a b Sakamoto KM, Kim KB, Kumagai A, Mercurio F, Crews CM, Deshaies RJ (July 2001). "Protacs: chimeric molecules that target proteins to the Skp1-Cullin-F box complex for ubiquitination and degradation". Proceedings of the National Academy of Sciences of the United States of America. 98 (15): 8554–8559. Bibcode:2001PNAS...98.8554S. doi:10.1073/pnas.141230798. PMC 37474. PMID 11438690.
  6. ^ Chi KR (May 2016). "Drug developers delve into the cell's trash-disposal machinery". Nature Reviews. Drug Discovery. 15 (5): 295–297. doi:10.1038/nrd.2016.86. PMID 27139985. S2CID 34652880.
  7. ^ Zengerle M, Chan KH, Ciulli A (August 2015). "Selective Small Molecule Induced Degradation of the BET Bromodomain Protein BRD4". ACS Chemical Biology. 10 (8): 1770–1777. doi:10.1021/acschembio.5b00216. PMC 4548256. PMID 26035625.
  8. ^ Bondeson DP, Mares A, Smith IE, Ko E, Campos S, Miah AH, et al. (August 2015). "Catalytic in vivo protein knockdown by small-molecule PROTACs". Nature Chemical Biology. 11 (8): 611–617. doi:10.1038/nchembio.1858. PMC 4629852. PMID 26075522.
  9. ^ Buckley DL, Raina K, Darricarrere N, Hines J, Gustafson JL, Smith IE, et al. (August 2015). "HaloPROTACS: Use of Small Molecule PROTACs to Induce Degradation of HaloTag Fusion Proteins". ACS Chemical Biology. 10 (8): 1831–1837. doi:10.1021/acschembio.5b00442. PMC 4629848. PMID 26070106.
  10. ^ Lu J, Qian Y, Altieri M, Dong H, Wang J, Raina K, et al. (June 2015). "Hijacking the E3 Ubiquitin Ligase Cereblon to Efficiently Target BRD4". Chemistry & Biology. 22 (6): 755–763. doi:10.1016/j.chembiol.2015.05.009. PMC 4475452. PMID 26051217.
  11. ^ Winter GE, Buckley DL, Paulk J, Roberts JM, Souza A, Dhe-Paganon S, et al. (June 2015). "DRUG DEVELOPMENT. Phthalimide conjugation as a strategy for in vivo target protein degradation". Science. 348 (6241): 1376–1381. doi:10.1126/science.aab1433. PMC 4937790. PMID 25999370.
  12. ^ Schneekloth AR, Pucheault M, Tae HS, Crews CM (November 2008). "Targeted intracellular protein degradation induced by a small molecule: En route to chemical proteomics". Bioorganic & Medicinal Chemistry Letters. 18 (22): 5904–5908. doi:10.1016/j.bmcl.2008.07.114. PMC 3175619. PMID 18752944.
  13. ^ Zhang X, Luukkonen LM, Eissler CL, Crowley VM, Yamashita Y, Schafroth MA, et al. (April 2021). "DCAF11 Supports Targeted Protein Degradation by Electrophilic Proteolysis-Targeting Chimeras". Journal of the American Chemical Society. 143 (13): 5141–5149. doi:10.1021/jacs.1c00990. PMC 8309050. PMID 33783207.
  14. ^ Xue G, Xie J, Hinterndorfer M, Cigler M, Dötsch L, Imrichova H, et al. (November 2023). "Discovery of a Drug-like, Natural Product-Inspired DCAF11 Ligand Chemotype". Nature Communications. 14 (1): 7908. Bibcode:2023NatCo..14.7908X. doi:10.1038/s41467-023-43657-6. PMC 10689823. PMID 38036533.
  15. ^ a b c d e f g Ocaña A, Pandiella A (September 2020). "Proteolysis targeting chimeras (PROTACs) in cancer therapy". Journal of Experimental & Clinical Cancer Research. 39 (1): 189. doi:10.1186/s13046-020-01672-1. PMC 7493969. PMID 32933565.
  16. ^ Itoh Y, Kitaguchi R, Ishikawa M, Naito M, Hashimoto Y (November 2011). "Design, synthesis and biological evaluation of nuclear receptor-degradation inducers". Bioorganic & Medicinal Chemistry. 19 (22): 6768–6778. doi:10.1016/j.bmc.2011.09.041. PMID 22014751.
  17. ^ "Connecticut to support New Haven biotech to the tune of $4.25 million". New Haven Register. 2013-09-26. Retrieved 2016-05-13.
  18. ^ "Scientist wants to hijack cells' tiny garbage trucks to fight cancer". Boston Globe. Retrieved 2016-05-21.
  19. ^ a b c d Schneider M, Radoux CJ, Hercules A, Ochoa D, Dunham I, Zalmas LP, et al. (October 2021). "The PROTACtable genome". Nature Reviews. Drug Discovery. 20 (10): 789–797. doi:10.1038/s41573-021-00245-x. PMID 34285415. S2CID 236157200.
  20. ^ a b c d 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. Bibcode:2021FrCh....9..215C. doi:10.3389/fchem.2021.672267. PMC 8093871. PMID 33959589.
  21. ^ "A Study of ARV-766 Given by Mouth in Men With Metastatic Prostate Cancer". ClinicalTrialsGov. NCT05067140.
  22. ^ a b Bondeson DP, Crews CM (January 2017). "Targeted Protein Degradation by Small Molecules". Annual Review of Pharmacology and Toxicology. 57: 107–123. doi:10.1146/annurev-pharmtox-010715-103507. PMC 5586045. PMID 27732798.
  23. ^ Schade M, Scott JS, Hayhow TG, Pike A, Terstiege I, Ahlqvist M, et al. (August 2024). "Structural and Physicochemical Features of Oral PROTACs". Journal of Medicinal Chemistry. 67 (15): 13106–13116. doi:10.1021/acs.jmedchem.4c01017. PMID 39078401.
  24. ^ Oughtred R, Rust J, Chang C, Breitkreutz BJ, Stark C, Willems A, et al. (January 2021). "The BioGRID database: A comprehensive biomedical resource of curated protein, genetic, and chemical interactions". Protein Science. 30 (1): 187–200. doi:10.1002/pro.3978. PMC 7737760. PMID 33070389.
  25. ^ Liu Y, Yang J, Wang T, Luo M, Chen Y, Chen C, et al. (October 2023). "Expanding PROTACtable genome universe of E3 ligases". Nature Communications. 14 (1): 6509. Bibcode:2023NatCo..14.6509L. doi:10.1038/s41467-023-42233-2. PMC 10579327. PMID 37845222.
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