Abstract
Protease-targeted chimeras (PROTACs) have been employed as a novel therapeutic approach, utilizing the ubiquitin-proteasome system for targeted protein degradation. PROTACs are heterobifunctional molecules consisting of an E3 ligase ligand and a small-molecule inhibitor for recruiting a protein of interest. After binding, PROTAC molecules recruit E3 ligase for ubiquitination of the protein of interest, which is followed by its proteasome-mediated degradation. PROTAC molecules have several advantages over traditional small-molecule inhibitors. A number of PROTAC molecules based on small-molecule inhibitors have been developed against various diseases, among which cereblon-based PROTAC molecules have received the greatest interest due to their promising clinical use. This article highlights the current trends in the discovery of cereblon-based PROTAC molecules along with their medicinal chemistry, clinical progression and future outlook in cancers, cardiovascular diseases and neurodegenerative disorders.
Papers of special note have been highlighted as: • of interest; •• of considerable interest
References
- 1. . Developing drugs for the ‘undruggable’. BioTechniques 69(4), 239–241 (2020).
- 2. . Understanding the metabolism of proteolysis targeting chimeras (PROTACs): the next step toward pharmaceutical applications. J. Med. Chem. 63(20), 11615–11638 (2020).
- 3. . Small-molecule PROTACs: an emerging and promising approach for the development of targeted therapy drugs. EBioMedicine 36, 553–562 (2018).
- 4. . Targeted protein degradation: elements of PROTAC design. Curr. Opin. Chem. Biol. 50, 111–119 (2019).
- 5. PROteolysis TArgeting Chimeras (PROTACs) as emerging anticancer therapeutics. Oncogene 39(26), 4909–4924 (2020).
- 6. Discovery of novel BCR-ABL PROTACs based on the cereblon E3 ligase design, synthesis, and biological evaluation. Eur. J. Med. Chem. 223, 113645 (2021).
- 7. Mutant-selective allosteric EGFR degraders are effective against a broad range of drug-resistant mutations. Angew Chem. Int. Ed. Engl. 59(34), 14481–14489 (2020).
- 8. Targeting the C481S ibrutinib-resistance mutation in Bruton's tyrosine kinase using PROTAC-mediated degradation. Biochemistry 57(26), 3564–3575 (2018).
- 9. AZD5438-PROTAC: a selective CDK2 degrader that protects against cisplatin- and noise-induced hearing loss. Eur. J. Med. Chem. 226, 113849 (2021). • References 5–9 highlight the advantages of the proteolysis targeting chimera approach over traditional small molecule inhibitors.
- 10. . MyD88: an adapter that recruits IRAK to the IL-1 receptor complex. Immunity 7(6), 837–847 (1997).
- 11. Design, synthesis, and biological evaluation of IRAK4-targeting PROTACs. ACS Med. Chem. Lett. 12(1), 82–87 (2021).
- 12. . E3 ligase ligands for PROTACs: how they were found and how to discover new ones. SLAS Discov. 26(4), 484–502 (2021).
- 13. . PROTACs: chimeric molecules that target proteins to the Skp1-Cullin-F box complex for ubiquitination and degradation. Proc. Natl Acad. Sci. USA 98(15), 8554–8559 (2001). •• This study provided the first example and discovery of a peptide-based proteolysis targeting chimera molecule.
- 14. Small-molecule inhibitors of the interaction between the E3 ligase VHL and HIF1alpha. Angew Chem. Int. Ed. Engl. 51(46), 11463–11467 (2012).
- 15. Targeting the von Hippel-Lindau E3 ubiquitin ligase using small molecules to disrupt the VHL/HIF-1alpha interaction. J. Am. Chem. Soc. 134(10), 4465–4468 (2012).
- 16. Catalytic in vivo protein knockdown by small-molecule PROTACs. Nat. Chem. Biol. 11(8), 611–617 (2015).
- 17. . Selective small molecule induced degradation of the BET bromodomain protein BRD4. ACS Chem. Biol. 10(8), 1770–1777 (2015). •• References 16 and 17 paved the way for the discovery of further proteolysis targeting chimera molecules based on small molecule inhibitors instead of peptide-based long proteolysis targeting chimeras.
- 18. Clinicaltrials.gov NCT03888612. Trial of ARV-110 in Patients with Metastatic Castration-Resistant Prostate Cancer. Available from: www.clinicaltrials.gov/ct2/show/NCT03888612?term=NCT03888612&draw=2&rank=1
- 19. Clinicaltrials.gov NCT04072952. A Phase 1/2 Trial of ARV-471 Alone and in Combination with Palbociclib (IBRANCE®) in Patients with ER+/HER2- Locally Advanced or Metastatic Breast Cancer. Available from: www.clinicaltrials.gov/ct2/show/NCT04072952?term=NCT04072952&draw=2&rank=1
- 20. Clinicaltrials.gov NCT05067140. Clinical Trial to Evaluate ARV-766 in Patients with Metastatic Castration-Resistant Prostate Cancer. Available from: www.clinicaltrials.gov/ct2/show/NCT05067140?term=NCT05067140&draw=2&rank=1
- 21. Clinicaltrials.gov NCT04886622. A Study of DT2216 in Relapsed/Refractory Malignancies. Available from: www.clinicaltrials.gov/ct2/show/NCT04886622?term=NCT04886622&draw=2&rank=1
- 22. Clinicaltrials.gov NCT04772885. A Single and Multiple Ascending Dose Trial of KT-474 in Healthy Adult Volunteers and Patients with Atopic Dermatitis (AD) or Hidradenitis Suppurativa (HS). Available from: www.clinicaltrials.gov/ct2/show/NCT04772885?term=NCT04772885&draw=2&rank=1
- 23. Clinicaltrials.gov NCT05233033. Safety, PK/PD, and Clinical Activity of KT-413 in Adult Patients with Relapsed or Refractory B-cell NHL. Available from: www.clinicaltrials.gov/ct2/show/NCT05233033?term=NCT05233033&draw=2&rank=1
- 24. Clinicaltrials.gov NCT05225584. Safety, PK, PD, Clinical Activity of KT-333 in Adult Patients with Refractory Lymphoma, Large Granular Lymphocytic Leukemia, Solid Tumors. Available from: www.clinicaltrials.gov/ct2/show/NCT05225584?term=NCT05225584&draw=2&rank=1
- 25. Clinicaltrials.gov NCT04830137. A Study of NX-2127 in Adults with Relapsed/Refractory B-cell Malignancies. Available from: www.clinicaltrials.gov/ct2/show/NCT04830137?term=NCT04830137&draw=2&rank=1
- 26. Clinicaltrials.gov NCT05131022. A Study of NX-5948 in Adults with Relapsed/Refractory B-cell Malignancies. Available from: www.clinicaltrials.gov/ct2/show/NCT05131022?term=NCT05131022&draw=2&rank=1
- 27. Clinicaltrials.gov NCT05355753. A Study to Assess the Safety and Tolerability of CFT8634 in Locally Advanced or Metastatic SMARCB1-Perturbed Cancers, Including Synovial Sarcoma and SMARCB1-Null Tumors. Available from: www.clinicaltrials.gov/ct2/show/NCT05355753?term=NCT05355753&draw=2&rank=1
- 28. Clinicaltrials.gov NCT04428788. Study to Evaluate the Safety and Tolerability of CC-94676 in Participants with Metastatic Castration-Resistant Prostate Cancer. Available from: www.clinicaltrials.gov/ct2/show/NCT04428788?term=NCT04428788&draw=2&rank=1
- 29. Clinicaltrials.gov NCT05080842. A Study of AC682 for the Treatment of Locally Advanced or Metastatic ER+ Breast Cancer. Available from: www.clinicaltrials.gov/ct2/show/NCT05080842?term=NCT05080842&draw=2&rank=1 • References 18–28 justify the clinical importance of proteolysis targeting chimera molecules against various disease conditions.
- 30. . Protein knockdown using methyl bestatin-ligand hybrid molecules: design and synthesis of inducers of ubiquitination-mediated degradation of cellular retinoic acid-binding proteins. J. Am. Chem. Soc. 132(16), 5820–5826 (2010).
- 31. Dissecting fragment-based lead discovery at the von Hippel-Lindau protein: hypoxia-inducible factor 1alpha protein-protein interface. Chem. Biol. 19(10), 1300–1312 (2012).
- 32. Structure-guided design and optimization of small molecules targeting the protein-protein interaction between the von Hippel-Lindau (VHL) E3 ubiquitin ligase and the hypoxia inducible factor (HIF) alpha subunit with in vitro nanomolar affinities. J. Med. Chem. 57(20), 8657–8663 (2014).
- 33. Group-based optimization of potent and cell-active inhibitors of the von Hippel-Lindau (VHL) E3 ubiquitin ligase: structure-activity relationships leading to the chemical probe (2S,4R)-1-((S)-2-(1-cyanocyclopropanecarboxamido)-3,3-dimethylbutanoyl)-4-hydroxy -N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (VH298). J. Med. Chem. 61(2), 599–618 (2018).
- 34. Potent and selective chemical probe of hypoxic signaling downstream of HIF-alpha hydroxylation via VHL inhibition. Nat. Commun. 7, 13312 (2016).
- 35. . Developments of CRBN-based PROTACs as potential therapeutic agents. Eur. J. Med. Chem. 225, 113749 (2021).
- 36. . Cereblon versus VHL: hijacking E3 ligases against each other using PROTACs. Bioorg. Med. Chem. 27(12), 2466–2479 (2019).
- 37. . Molecular mechanisms of thalidomide and its derivatives. Proc. Jpn Acad. Ser. B Phys. Biol. Sci. 96(6), 189–203 (2020).
- 38. Identification of a primary target of thalidomide teratogenicity. Science 327(5971), 1345–1350 (2010).
- 39. . Identification and functional characterization of cereblon as a binding protein for large-conductance calcium-activated potassium channel in rat brain. J. Neurochem. 94(5), 1212–1224 (2005).
- 40. . Glutamine and cancer: cell biology, physiology, and clinical opportunities. J. Clin. Invest. 123(9), 3678–3684 (2013).
- 41. . Q's next: the diverse functions of glutamine in metabolism, cell biology and cancer. Oncogene 29(3), 313–324 (2010).
- 42. Glutamine triggers acetylation-dependent degradation of glutamine synthetase via the thalidomide receptor cereblon. Mol. Cell 61(6), 809–820 (2016).
- 43. . Targeted intracellular protein degradation induced by a small molecule: en route to chemical proteomics. Bioorg. Med. Chem. Lett. 18(22), 5904–5908 (2008).
- 44. PROTACs: a novel strategy for cancer therapy. Semin. Cancer Biol. 67(Pt 2), 171–179 (2020).
- 45. 3-Fluoro-4-hydroxyprolines: synthesis, conformational analysis, and stereoselective recognition by the VHL E3 ubiquitin ligase for targeted protein degradation. J. Am. Chem. Soc. 140(29), 9299–9313 (2018).
- 46. . PROTAC: a promising technology for cancer treatment. Eur. J. Med. Chem. 203, 112539 (2020).
- 47. PROTACs: great opportunities for academia and industry (an update from 2020 to 2021). Signal Transduct. Target Ther. 7(1), 181 (2022).
- 48. . Design and pharmaceutical applications of proteolysis-targeting chimeric molecules. Biochem. Pharmacol. 182, 114211 (2020).
- 49. . Progress on small-molecule proteolysis-targeting chimeras. Future Med. Chem. 11(20), 2715–2734 (2019).
- 50. Discovery of a PROTAC targeting ALK with in vivo activity. Eur. J. Med. Chem. 212, 113150 (2021).
- 51. Structure-based discovery of SIAIS001 as an oral bioavailability ALK degrader constructed from Alectinib. Eur. J. Med. Chem. 217, 113335 (2021).
- 52. Discovery of A031 as effective proteolysis targeting chimera (PROTAC) androgen receptor (AR) degrader for the treatment of prostate cancer. Eur. J. Med. Chem. 216, 113307 (2021).
- 53. Chemical degradation of androgen receptor (AR) using bicalutamide analog-thalidomide PROTACs. Molecules 26(9), 2525 (2021).
- 54. . Construction of an IMiD-based azide library as a kit for PROTAC research. Org. Biomol. Chem. 19(1), 166–170 (2021).
- 55. Targeted degradation of the enhancer lysine acetyltransferases CBP and p300. Cell. Chem. Biol. 28(4), 503–514 e512 (2021).
- 56. Fusion of MOZ and p300 histone acetyltransferases in acute monocytic leukemia with a t(8;22)(p11;q13) chromosome translocation. Leukemia 15(1), 89–94 (2001).
- 57. The leukemogenicity of AML1-ETO is dependent on site-specific lysine acetylation. Science 333(6043), 765–769 (2011).
- 58. . Exploitation of EP300 and CREBBP lysine acetyltransferases by cancer. Cold Spring Harb. Perspect. Med. 7(3), a026534 (2017).
- 59. Discovery of a first-in-class CDK2 selective degrader for AML differentiation therapy. Nat Chem. Biol. 17(5), 567–575 (2021).
- 60. Selective degradation of CDK6 by a palbociclib based PROTAC. Bioorg. Med. Chem. Lett. 29(11), 1375–1379 (2019).
- 61. Discovery of selective CDK9 degraders with enhancing antiproliferative activity through PROTAC conversion. Eur. J. Med. Chem. 211, 113091 (2021).
- 62. Aminopyrazole-based CDK9 PROTAC sensitizes pancreatic cancer cells to venetoclax. Bioorg. Med. Chem. Lett. 43, 128061 (2021).
- 63. First orally bioavailable prodrug of proteolysis targeting chimera (PROTAC) degrades cyclin-dependent kinases 2/4/6 in vivo. Eur. J. Med. Chem. 209, 112903 (2021).
- 64. . Multivalent feedback regulation of HMG CoA reductase, a control mechanism coordinating isoprenoid synthesis and cell growth. J. Lipid Res. 21(5), 505–517 (1980).
- 65. . Statin intolerance. Rev. Cardiovasc. Med. 19(S1), S9–S19 (2018).
- 66. Degradation versus inhibition: development of proteolysis-targeting chimeras for overcoming statin-induced compensatory upregulation of 3-hydroxy-3-methylglutaryl coenzyme A reductase. J. Med. Chem. 63(9), 4908–4928 (2020).
- 67. . Structural and functional characterization of HQL-79, an orally selective inhibitor of human hematopoietic prostaglandin D synthase. J. Biol. Chem. 281(22), 15277–15286 (2006).
- 68. Development of a hematopoietic prostaglandin D synthase-degradation inducer. ACS Med. Chem. Lett. 12(2), 236–241 (2021).
- 69. . Glycogen synthase kinase-3 (GSK3): regulation, actions, and diseases. Pharmacol. Ther. 148, 114–131 (2015).
- 70. Glycogen synthase kinase-3 beta (GSK-3beta) signaling: Implications for Parkinson's disease. Pharmacol. Res. 97, 16–26 (2015).
- 71. PROTACs suppression of GSK-3beta, a crucial kinase in neurodegenerative diseases. Eur. J. Med. Chem. 210, 112949 (2021).
- 72. . The druggable genome. Nat. Rev. Drug Discov. 1(9), 727–730 (2002).