PROTAC^® technology and potential for its application in infection control

Objectives. To describe the pharmaceutical technology of controlled degradation of protein molecules (PROTAC^®, Proteolysis Targeting Chimera), approaches to the design of the PROTAC^® molecule, methods of ligand and linker selection and synthesis, as well as the application of this technology in dealing with a variety of diseases and the possible limitations of its use.
Results. The review covers 77 sources, mostly from 2020–2023. The review outlines the principle of PROTAC^® technology: the construction of a chimeric molecule consisting of three fragments. One fragment specifically binds to the biotarget, another recruits the proteolytic system of the host cell, and the third binds them together. The main areas of the current development of the technology are described herein, as well as the opportunities and limitations of chimeric molecules in the fight against different types of infectious diseases.
Conclusion. The potential to use PROTAC^® technology to combat cancer as well as neurodegenerative, autoimmune, and infectious diseases is shown.

1. Sakamoto K.M., Kim K.B., Kumagai A., Mercurio F., Crews C.M., Deshaies R.J. Protacs: chimeric molecules that target proteins to the Skp1-Cullin-F box complex for ubiquitination and degradation. Proc. Natl. Acad. Sci. U S A. 2001;98(15):8554–8559. https://doi.org/10.1073/pnas.141230798

2. Kleiger G., Mayor T. Perilous journey: a tour of the ubiquitinproteasome system. Trends Cell Biol. 2014;24(6):352–359. https://doi.org/10.1016/j.tcb.2013.12.003

3. Bekes M., Langley D.R., Crews C.M. PROTAC targeted protein degraders: the past is prologue. Nat. Rev. Drug Discov. 2022;21(3):181–200. https://doi.org/10.1038/s41573-021-00371-6

4. He M., Cao C., Ni Z., Liu Y., Song P., Hao S., et al. PROTACs: great opportunities for academia and industry (an update from 2020 to 2021). Signal Transduct. Target. Ther. 2022;7(1):181. https://doi.org/10.1038/s41392-022-00999-9

5. Koroleva O.A., Dutikova Yu.V., Trubnikov A.V., et al. PROTAC: targeted drug strategy. Principles and limitations. Russ. Chem. Bull. https://doi.org/10.1007/s11172-022-3659-z [Original Russian Text: Koroleva O.A., Dutikova Yu.V., Trubnikov A.V., Zenov F.A., Manasova E.V., Shtil’ A.A., Kurkin A.V. PROTAC: targeted drug strategy. Principles and limitations. Izvestiya Akademii Nauk. Seriya khimicheskaya. 2022;71(11):2310–2334 (in Russ.).]

6. Cao C., He M., Wang L., He Y., Rao Y. Chemistries of bifunctional PROTAC degraders. Chem. Soc. Rev. 2022;51(16):7066–7114. https://doi.org/10.1039/d2cs00220e

7. Liu Z., Hu M., Yang Y., Du C., Zhou H., Liu C., et al. An overview of PROTACs: a promising drug discovery paradigm. Mol. Biomed. 2022;3(1):46. https://doi.org/10.1186/s43556-022-00112-0

8. Yang N., Kong B., Zhu Z., Huang F., Zhang L., Lu T., et al. Recent advances in targeted protein degraders as potential therapeutic agents. Mol. Divers. 2024;28:309–333. https://doi.org/10.1007/s11030-023-10606-w

9. Li S., Chen T., Liu J., Zhang H., Li J., Wang Z., et al. PROTACs: Novel tools for improving immunotherapy in cancer. Cancer Lett. 2023;560:216128. https://doi.org/10.1016/j.canlet.2023.216128

10. Guedeney N., Cornu M., Schwalen F., Kieffer C., Voisin-Chiret A.S. PROTAC technology: A new drug design for chemical biology with many challenges in drug discovery. Drug Discov. Today. 2023;28(1):103395. https://doi.org/10.1016/j.drudis.2022.103395

11. Bricelj A., Steinebach C., Kuchta R., Gutschow M., Sosic I. E3 Ligase Ligands in Successful PROTACs: An Overview of Syntheses and Linker Attachment Points. Front. Chem. 2021;9:707317. https://doi.org/10.3389/fchem.2021.707317

12. Chamberlain P.P., Lopez-Girona A., Miller K., Carmel G., Pagarigan B., Chie-Leon B., et al. Structure of the human Cereblon-DDB1-lenalidomide complex reveals basis for responsiveness to thalidomide analogs. Nat. Struct. Mol. Biol. 2014;21(9):803–809. https://doi.org/10.1038/nsmb.2874

13. Simpson L.M., Glennie L., Brewer A., Zhao J.F., Crooks J., Shpiro N., et al. Target protein localization and its impact on PROTAC-mediated degradation. Cell Chem. Biol. 2022;29(10):1482–1504.e7. https://doi.org/10.1016/j.chembiol.2022.08.004

14. Shah V.J., Đikić I. Localization matters in targeted protein degradation. Cell Chem. Biol. 2022;29(10):1465–1466. https://doi.org/10.1016/j.chembiol.2022.09.006

15. Bemis T.A., La Clair J.J., Burkart M.D. Unraveling the Role of Linker Design in Proteolysis Targeting Chimeras. J. Med. Chem. 2021;64(12):8042–8052. https://doi.org/10.1021/acs.jmedchem.1c00482

16. Gadd M.S., Testa A., Lucas X., Chan K.H., Chen W., Lamont D.J., et al. Structural basis of PROTAC cooperative recognition for selective protein degradation. Nat. Chem. Biol. 2017;13(5):514–521. https://doi.org/10.1038/nchembio.2329

17. Cao C., Yang J., Chen Y., Zhou P., Wang Y., Du W., et al. Discovery of SK-575 as a Highly Potent and Efficacious Proteolysis-Targeting Chimera Degrader of PARP1 for Treating Cancers. J. Med. Chem. 2020;63(19):11012–11033. https://doi.org/10.1021/acs.jmedchem.0c00821

18. Carmony K.C., Kim K.B. PROTAC-induced proteolytic targeting. In: Dohmen R., Scheffner M. (Eds.). Ubiquitin Family Modifiers and the Proteasome. Methods in Molecular Biology. Humana Press; 2012. V. 832. P. 627–638. https://doi.org/10.1007/978-1-61779-474-2_4419

19. Bondeson D.P., Smith B.E., Burslem G.M., Buhimschi A.D., Hines J., Jaime-Figueroa S., et al. Lessons in PROTAC Design from Selective Degradation with a Promiscuous Warhead. Cell Chem. Biol. 2018;25(1):78–87.e5. https://doi.org/10.1016/j.chembiol.2017.09.010

20. Paiva S.L., Crews C.M. Targeted protein degradation: elements of PROTAC design. Curr. Opin. Chem. Biol. 2019;50:111–119. https://doi.org/10.1016/j.cbpa.2019.02.022

21. Rao Z., Li K., Hong J., Chen D., Ding B., Jiang L., et al. A practical “preTACs-cytoblot” platform accelerates the streamlined development of PROTAC-based protein degraders. Eur. J. Med. Chem. 2023;251:115248. https://doi.org/10.1016/j.ejmech.2023.115248

22. Guo L., Zhou Y., Nie X., Zhang Z., Zhang Z., Li C., et al. A platform for the rapid synthesis of proteolysis targeting chimeras (Rapid-TAC) under miniaturized conditions. Eur. J. Med. Chem. 2022;236:114317. https://doi.org/10.1016/j.ejmech.2022.114317

23. Bhela I.P., Ranza A., Balestrero F.C., Serafini M., Aprile S., Di Martino R.M.C., et al. A Versatile and Sustainable Multicomponent Platform for the Synthesis of Protein Degraders: Proof-of-Concept Application to BRD4-Degrading PROTACs. J. Med Chem. 2022;65(22):15282–15299. https://doi.org/10.1021/acs.jmedchem.2c01218

24. Liu Z., ZhangY., XiangY., Kang X. Small-Molecule PROTACs for Cancer Immunotherapy. Molecules. 2022;27(17):5439. https://doi.org/10.3390/molecules27175439

25. Li J., Chen X., Lu A., Liang C. Targeted protein degradation in cancers: Orthodox PROTACs and beyond. The Innovation. 2023;4(3):100413. https://doi.org/10.1016/j.xinn.2023.100413

26. Yedla P., BabalghithA.O., AndraV.V., Syed R. PROTACs in the Management of Prostate Cancer. Molecules. 2023;28(9):3698. https://doi.org/10.3390/molecules28093698

27. Gao X., Burris Iii H.A., Vuky J., Dreicer R., Sartor A.O., Sternberg C.N., et al. Phase 1/2 study of ARV-110, an androgen receptor (AR) PROTAC degrader, in metastatic castration-resistant prostate cancer (mCRPC). J. Clin. Oncol. 2022;40(6_suppl):17–17. https://doi.org/10.1200/JCO.2022.40.6_suppl.017

28. Ha S., Luo G., Xiang H. A Comprehensive Overview of Small-Molecule Androgen Receptor Degraders: Recent Progress and Future Perspectives. J. Med. Chem. 2022;65(24):16128–16154. https://doi.org/10.1021/acs.jmedchem.2c01487

29. Hamilton E.P., Schott A.F., Nanda R., Lu H., Keung C.F., Gedrich R., et al. ARV-471, an estrogen receptor (ER) PROTACdegrader, combined with palbociclib in advanced ER+/human epidermal growth factor receptor 2–negative (HER2-) breast cancer: Phase 1b cohort (part C) of a phase 1/2 study. J. Clin. Oncol. 2022;40(16_suppl):TPS1120–TPS1120. https://doi.org/10.1200/JCO.2022.40.16_suppl.TPS1120

30. Xu H., Ohoka N., Yokoo H., Nemoto K., Ohtsuki T., Matsufuji H., et al. Development of Agonist-Based PROTACs Targeting Liver X Receptor. Front. Chem. 2021;9:674967. https://doi.org/10.3389/fchem.2021.674967

31. Yu F., Cai M., Shao L., Zhang J. Targeting Protein Kinases Degradation by PROTACs. Front. Chem. 2021;9:679120. https://doi.org/10.3389/fchem.2021.679120

32. Dikic I., Elazar Z. Mechanism and medical implications of mammalian autophagy. Nat. Rev. Mol. Cell Biol. 2018;19(6):349–364. https://doi.org/10.1038/s41580-018-0003-4

33. TakahashiD., MoriyamaJ., NakamuraT., MikiE., TakahashiE., Sato A., et al. AUTACs: Cargo-Specific Degraders Using Selective Autophagy. Mol. Cell. 2019;76(5):797–810.e10. https://doi.org/10.1016/j.molcel.2019.09.009

34. Li X., Liu Q., Xie X., Peng C., Pang Q., Liu B., et al. Application of Novel Degraders Employing Autophagy for Expediting Medicinal Research. J. Med. Chem. 2023;66(3):1700–1711. https://doi.org/10.1021/acs.jmedchem.2c01712

35. Li Z., Ma S., Zhang L., Zhang S., Ma Z., Du L., et al. Targeted Protein Degradation Induced by HEMTACs Based on HSP90. J. Med. Chem. 2023;66(1):733–751. https://doi.org/10.1021/acs.jmedchem.2c01648

36. Brown K.J., Seol H., Pillai D.K., Sankoorikal B.J., Formolo C.A., Mac J., et al. The human secretome atlas initiative: implications in health and disease conditions. Biochim. Biophys. Acta. 2013;1834(11):2454–2461. https://doi.org/10.1016/j.bbapap.2013.04.007

37. Banik S.M., Pedram K., Wisnovsky S., Ahn G., Riley N.M., Bertozzi C.R. Lysosome-targeting chimaeras for degradation of extracellular proteins. Nature. 2020;584(7820):291–297. https://doi.org/10.1038/s41586-020-2545-9

38. Caianiello D.F., Zhang M., Ray J.D., Howell R.A., Swartzel J.C., Branham E.M.J., et al. Bifunctional small molecules that mediate the degradation of extracellular proteins. Nat. Chem. Biol. 2021;17(9):947–953. https://doi.org/10.1038/s41589-021-00851-1

39. Ahn G., Banik S.M., Miller C.L., Riley N.M., Cochran J.R., Bertozzi C.R. LYTACs that engage the asialoglycoprotein receptor for targeted protein degradation. Nat. Chem. Biol. 2021;17(9):937–946. https://doi.org/10.1038/s41589-021-00770-1

40. Wu Y., Lin B., Lu Y., Li L., Deng K., Zhang S., et al. Aptamer-LYTACs for Targeted Degradation of Extracellular and Membrane Proteins. Angew. Chem. Int. Ed. Engl. 2023;62(15):e202218106. https://doi.org/10.1002/anie.202218106

41. Kong L., Meng F., Wu S., Zhou P., Ge R., Liu M., et al. Selective degradation of the p53-R175H oncogenic hotspot mutant by an RNA aptamer-based PROTAC. Clin. Transl. Med. 2023;13(2):e1191. https://doi.org/10.1002/ctm2.1191

42. Dey S.K., Jaffrey S.R. RIBOTACs: Small Molecules Target RNA for Degradation. Cell Chem. Biol. 2019;26(8): 1047–1049. https://doi.org/10.1016/j.chembiol.2019.07.015

43. Childs-Disney J.L., Yang X., Gibaut Q.M.R., Tong Y., Batey R.T., Disney M.D. Targeting RNA structures with small molecules. Nat. Rev. Drug Discov. 2022;21(10):736–762. https://doi.org/10.1038/s41573-022-00521-4

44. Costales M.G., Suresh B., Vishnu K., Disney M.D. Targeted Degradation of a Hypoxia-Associated Non-coding RNA Enhances the Selectivity of a Small Molecule Interacting with RNA. Cell Chem. Biol. 2019;26(8):1180–1186e5. https://doi.org/10.1016/j.chembiol.2019.04.008

45. Borgelt L., Haacke N., Lampe P., Qiu X., Gasper R., Schiller D., et al. Small-molecule screening of ribonuclease L binders for RNA degradation. Biomed. Pharmacother. 2022;154:113589. https://doi.org/10.1016/j.biopha.2022.113589

46. Ma S., Ji J., Tong Y., Zhu Y., Dou J., Zhang X., et al. Non-small molecule PROTACs (NSM-PROTACs): Protein degradation kaleidoscope. Acta Pharm. Sin. B. 2022;12(7):2990–3005. https://doi.org/10.1016/j.apsb.2022.02.022

47. Gao H., Sun X., Rao Y. PROTAC Technology: Opportunities and Challenges. ACS Med. Chem. Lett. 2020;11(3):237–240. https://doi.org/10.1021/acsmedchemlett.9b00597

48. O’Brien Laramy M.N., Luthra S., Brown M.F., Bartlett D.W. Delivering on the promise of protein degraders. Nat. Rev. Drug Discov. 2023;22(5):410–427. https://doi.org/10.1038/s41573-023-00652-2

49. Cecchini C., Pannilunghi S., Tardy S., Scapozza L. From Conception to Development: Investigating PROTACs Features for Improved Cell Permeability and Successful Protein Degradation. Front. Chem. 2021;9:672267. https://doi.org/10.3389/fchem.2021.672267

50. Liu X., Zhang X., Lv D., Yuan Y., Zheng G., Zhou D. Assays and technologies for developing proteolysis targeting chimera degraders. Future Med. Chem. 2020;12(12):1155–1179. https://doi.org/10.4155/fmc-2020-0073

51. Pfaff P., Samarasinghe K.T.G., Crews C.M., Carreira E.M. Reversible Spatiotemporal Control of Induced Protein Degradation by Bistable PhotoPROTACs. ACS Cent. Sci. 2019;5(10): 1682–1690. https://doi.org/10.1021/acscentsci.9b00713

52. Zeng S., Zhang H., Shen Z., Huang W. Photopharmacology of Proteolysis-Targeting Chimeras: A New Frontier for Drug Discovery. Front. Chem. 2021;9:639176. https://doi.org/10.3389/fchem.2021.639176

53. Liu J., Chen H., Liu Y., Shen Y., Meng F., Kaniskan H.U., et al. Cancer Selective Target Degradation by Folate-Caged PROTACs. J. Am. Chem. Soc. 2021;143(19):7380–7387. https://doi.org/10.1021/jacs.1c00451

54. Gabizon R., Shraga A., Gehrtz P., Livnah E., Shorer Y., Gurwicz N., et al. Efficient Targeted Degradation via Reversible and Irreversible Covalent PROTACs. J. Am. Chem. Soc. 2020;142(27):11734–11742. https://doi.org/10.1021/jacs.9b13907

55. Yuan M., Chu Y., Duan Y. Reversible Covalent PROTACs: Novel and Efficient Targeted Degradation Strategy. Front. Chem. 2021;9:691093. https://doi.org/10.3389/fchem.2021.691093

56. Jin Y., Fan J., Wang R., Wang X., Li N., You Q., et al. Ligation to Scavenging Strategy Enables On-Demand Termination of Targeted Protein Degradation. J. Am. Chem. Soc. 2023;145(13):7218–7229. https://doi.org/10.1021/jacs.2c12809

57. Morreale F.E., Kleine S., Leodolter J., Junker S., Hoi D.M., Ovchinnikov S., et al. BacPROTACs mediate targeted protein degradation in bacteria. Cell. 2022;185(13):2338–2353e18. https://doi.org/10.1016/j.cell.2022.05.009

58. Gopal P., Dick T. Targeted protein degradation in antibacterial drug discovery? Prog. Biophys. Mol. Biol. 2020;152:10–14. https://doi.org/10.1016/j.pbiomolbio.2019.11.005

59. SarathyJ.P., AldrichC.C., GoM.L., DickT. PROTAC antibiotics: the time is now. Expert Opin. Drug Discov. 2023;18(4): 363–370. https://doi.org/10.1080/17460441.2023.2178413

60. Venkatesan J., Murugan D., Rangasamy L. A Perspective on Newly Emerging Proteolysis-Targeting Strategies in Antimicrobial Drug Discovery. Antibiotics (Basel). 2022;11(12):1717. https://doi.org/10.3390/antibiotics11121717

61. Espinoza-Chavez R.M., Salerno A., Liuzzi A., Ilari A., Milelli A., Uliassi E., et al. Targeted Protein Degradation for Infectious Diseases: from Basic Biology to Drug Discovery. ACS Bio Med. Chem. Au. 2023;3(1):32–45. https://doi.org/10.1021/acsbiomedchemau.2c00063

62. Desantis J., Goracci L. Proteolysis targeting chimeras in antiviral research. Future Med. Chem. 2022;14(7):459–462. https://doi.org/10.4155/fmc-2022-0005

63. Ma Y., Frutos-Beltran E., Kang D., Pannecouque C., De Clercq E., Menendez-Arias L., et al. Medicinal chemistry strategies for discovering antivirals effective against drugresistant viruses. Chem. Soc. Rev. 2021;50(7):4514–4540. https://doi.org/10.1039/d0cs01084g

64. Reboud-Ravaux M., ElAmri C. COVID-19 Therapies: Protease Inhibitions and Novel Degrader Strategies. Front. Drug Discov. 2022;2. https://doi.org/10.3389/fddsv.2022.892057

65. Li H., Wang S., Ma W., Cheng B., Yi Y., Ma X., et al. Discovery of Pentacyclic Triterpenoid PROTACs as a Class of Effective Hemagglutinin Protein Degraders. J. Med. Chem. 2022;65(10):7154–7169. https://doi.org/10.1021/acs.jmedchem.1c02013

66. Li W., Yang F., Meng L., Sun J., Su Y., Shao L., et al. Synthesis, Structure Activity Relationship and Anti-influenza A Virus Evaluation of Oleanolic Acid-Linear Amino Derivatives. Chem. Pharm. Bull. (Tokyo). 2019;67(11):1201–1207. https://doi.org/10.1248/cpb.c19-00485

67. Xu Z., Liu X., Ma X., Zou W., Chen Q., Chen F., et al. Discovery of oseltamivir-based novel PROTACs as degraders targeting neuraminidase to combat H1N1 influenza virus. Cell Insight. 2022;1(3):100030. https://doi.org/10.1016/j.cellin.2022.100030

68. De Wispelaere M., Du G., Donovan K.A., Zhang T., Eleuteri N.A., Yuan J.C., et al. Small molecule degraders of the hepatitis C virus protease reduce susceptibility to resistance mutations. Nat. Commun. 2019;10(1):3468. https://doi.org/10.1038/s41467-019-11429-w

69. Haniff H.S., Tong Y., Liu X., Chen J.L., Suresh B.M., Andrews R.J., et al. Targeting the SARS-CoV-2 RNA Genome with Small Molecule Binders and Ribonuclease Targeting Chimera (RIBOTAC) Degraders. ACS Cent. Sci. 2020;6(10):1713–1721. https://doi.org/10.1021/acscentsci.0c00984

70. Su X., Ma W., Feng D., Cheng B., Wang Q., Guo Z., et al. Efficient Inhibition of SARS-CoV-2 Using Chimeric Antisense Oligonucleotides through RNase L Activation. Angew. Chem. Int. Ed. Engl. 2021;60(40):21662–21667. https://doi.org/10.1002/anie.202105942

71. Zhou Y., Zheng R., Liu D., Liu S., Disoma C., Li S., et al. UBR5 Acts as an Antiviral Host Factor against MERS-CoV via Promoting Ubiquitination and Degradation of ORF4b. J. Virol. 2022;96(17):e0074122. https://doi.org/10.1128/jvi.00741-22

72. Zhao J., Wang J., Pang X., Liu Z., Li Q., Yi D., et al. An antiinfluenza A virus microbial metabolite acts by degrading viral endonuclease PA. Nat. Commun. 2022;13(1):2079. https://doi.org/10.1038/s41467-022-29690-x

73. Wild M., Kicuntod J., Seyler L., Wangen C., Bertzbach L.D., Conradie A.M., et al. Combinatorial Drug Treatments Reveal Promising Anticytomegaloviral Profiles for Clinically Relevant Pharmaceutical Kinase Inhibitors (PKIs). Int. J. Mol. Sci. 2021;22(2):575. https://doi.org/10.3390/ijms22020575

74. Hahn F., Hamilton S.T., Wangen C., Wild M., Kicuntod J., Bruckner N., et al. Development of a PROTAC-Based Targeting Strategy Provides a Mechanistically Unique Mode of Anti-Cytomegalovirus Activity. Int. J. Mol. Sci. 2021;22(23):12858. https://doi.org/10.3390/ijms222312858

75. Desantis J., Mercorelli B., Celegato M., Croci F., Bazzacco A., Baroni M., et al. Indomethacin-based PROTACs as pan-coronavirus antiviral agents. Eur. J. Med. Chem. 2021;226:113814. https://doi.org/10.1016/j.ejmech.2021.113814

76. Zahid S., Ali Y., Rashid S. Structural-based design of HD-TAC7 PROteolysis TArgeting chimeras (PROTACs) candidate transformations to abrogate SARS-CoV-2 infection. J. Biomol. Struct. Dyn. 2023;41(23):14566–14581. https://doi.org/10.1080/07391102.2023.2183037

77. Shaheer M., Singh R., Sobhia M.E. Protein degradation: a novel computational approach to design protein degrader probes for main protease of SARS-CoV-2. J. Biomol. Struct. Dyn. 2022;40(21):10905–10917. https://doi.org/10.1080/07391102.2021.1953601