Citation: Yangwode Jing, Chong Zuo, Yun-Xiang Du, Junxiong Mao, Ruichao Ding, Jiachen Zhang, Lu-Jun Liang, Qian Qu. Chemical tools for E3 ubiquitin ligase study[J]. Chinese Chemical Letters, ;2023, 34(4): 107781. doi: 10.1016/j.cclet.2022.107781 shu

Chemical tools for E3 ubiquitin ligase study

Yangwode Jing ^{a, b} ,
Chong Zuo ^b ,
Yun-Xiang Du ^b ,
Junxiong Mao ^b ,
Ruichao Ding ^b ,
Jiachen Zhang ^b ,
Lu-Jun Liang ^b ,
Qian Qu ^{a, *,}

a.
Institute of Translational Medicine, Shanghai Jiao Tong University, Shanghai 200240, China
b.
Tsinghua-Peking Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China

quqian22@sjtu.edu.cn

Received Date: 14 June 2022
Revised Date: 17 August 2022
Accepted Date: 23 August 2022
Available Online: 28 August 2022

Figures(9)

E3 ubiquitin ligases catalyze the final step of ubiquitylation, a crucial post-translational modification involved in almost every process in eukaryotic cells. E3 ubiquitin ligases are key regulators of cellular events, and the investigation into their functions and functioning mechanisms are research areas with great importance. Synthetic or semi-synthetic tools have greatly facilitated the research about the enzyme activity, distribution in different physiological events, and catalytic mechanism of E3 ubiquitin ligase. In this review, we summarize the development of chemical tools for E3 ubiquitin ligases with an emphasis on the synthetic routes. We show the utility of these chemical tools by briefly discussing their applications in biological research.
- Chemical tools,
- Protein chemical synthesis,
- Ubiquitylation,
- E3 ligase,
- Enzymatic mechanism
1. [1]
  D. Komander, M. Rape, Annu. Rev. Biochem. 81 (2012) 203–229. doi: 10.1146/annurev-biochem-060310-170328
2. [2]
  A. Hershko, A. Ciechanover, Annu. Rev. Biochem. 67 (1998) 425–479. doi: 10.1146/annurev.biochem.67.1.425
3. [3]
  L. Buetow, D.T. Huang, Nat. Rev. Mol. Cell Biol. 17 (2016) 626–642. doi: 10.1038/nrm.2016.91
4. [4]
  C.E. Berndsen, C. Wolberger, Nat. Rev. Mol. Cell Biol. 21 (2014) 301–307.
5. [5]
  R.J. Deshaies, C.A. Joazeiro, Annu. Rev. Biochem. 78 (2009) 399–434. doi: 10.1146/annurev.biochem.78.101807.093809
6. [6]
  D. Rotin, S. Kumar, Nat. Rev. Mol. Cell Biol. 10 (2009) 398–409. doi: 10.1038/nrm2690
7. [7]
  H. Walden, K. Rittinger, Nat. Struct. Mol. Biol. 25 (2018) 440–445. doi: 10.1038/s41594-018-0063-3
8. [8]
  H.D. Ulrich, H. Walden, Nat. Rev. Mol. Cell Biol. 11 (2010) 479–489. doi: 10.1038/nrm2921
9. [9]
  K.S. McNaught, C.W. Olanow, B. Halliwell, O. Isacson, P. Jenner, Nat. Rev. Neurosci. 2 (2001) 589–594. doi: 10.1038/35086067
10. [10]
  B. Dale, M. Cheng, K.S. Park, et al., Nat. Rev. Cancer 21 (2021) 638–654. doi: 10.1038/s41568-021-00365-x
11. [11]
  Z.J. Chen, Nat. Cell Biol. 7 (2005) 758–765. doi: 10.1038/ncb0805-758
12. [12]
  H. Ashida, M. Kim, C. Sasakawa, Nat. Rev. Microbiol. 12 (2014) 399–413. doi: 10.1038/nrmicro3259
13. [13]
  A. Craney, M. Rape, Curr. Opin. Cell Biol. 25 (2013) 704–710. doi: 10.1016/j.ceb.2013.07.004
14. [14]
  D.S. Hewings, J.A. Flygare, M. Bogyo, I.E. Wertz, FEBS J. 284 (2017) 1555–1576. doi: 10.1111/febs.14039
15. [15]
  K.F. Witting, M. Mulder, H. Ovaa, J. Mol. Biol. 429 (2017) 3388–3394. doi: 10.1016/j.jmb.2017.04.002
16. [16]
  K.C. Pao, N.T. Wood, A. Knebel, et al., Nature 556 (2018) 381–385. doi: 10.1038/s41586-018-0026-1
17. [17]
  L.J. Liang, G.C. Chu, Q. Qu, et al., Angew. Chem. Int. Ed. 60 (2021) 2–9. doi: 10.1002/anie.202014556
18. [18]
  L.A. Carpino, J. Am. Chem. Soc. 92 (1970) 5748. doi: 10.1021/ja00722a043
19. [19]
  C.D. Chang, J. Meienhofer, Int. J. Pept. Protein Res. 11 (1978) 246–249.
20. [20]
  P.E. Dawson, T.W. Muir, I. Clark-Lewis, S.B.H. Kent, Science 266 (1994) 776. doi: 10.1126/science.7973629
21. [21]
  Q. Wan, S.J. Danishefsky, Angew. Chem. Int. Ed. 46 (2007) 9248–9252. doi: 10.1002/anie.200704195
22. [22]
  G.M. Fang, Y.M. Li, F. Shen, et al., Angew. Chem. Int. Ed. 50 (2011) 7645–7649. doi: 10.1002/anie.201100996
23. [23]
  G.M. Fang, J.X. Wang, L. Liu, Angew. Chem. Int. Ed. 51 (2012) 10347–10350. doi: 10.1002/anie.201203843
24. [24]
  S. Tang, Y.Y. Si, Z.P. Wang, et al., Angew. Chem. Int. Ed. 54 (2015) 5713–5717. doi: 10.1002/anie.201500051
25. [25]
  Y. Zhang, C. Xu, H.Y. Lam, C.L. Lee, X. Li, Proc. Natl. Acad. Sci. U. S. A. 110 (2013) 6657–6662. doi: 10.1073/pnas.1221012110
26. [26]
  J.W. Bode, R.M. Fox, K.D. Baucom, Angew. Chem. Int. Ed. 45 (2006) 1248–1252. doi: 10.1002/anie.200503991
27. [27]
  J. Shi, T.W. Muir, J. Am. Chem. Soc. 127 (2005) 6198–6206. doi: 10.1021/ja042287w
28. [28]
  Y.M. Li, Y.T. Li, M. Pan, et al., Angew. Chem. Int. Ed. 53 (2014) 2198–2202. doi: 10.1002/anie.201310010
29. [29]
  G.C. Chu, M. Pan, J. Li, et al., J. Am. Chem. Soc. 141 (2019) 3654–3663. doi: 10.1021/jacs.8b13213
30. [30]
  Y. Gao, A. Koppen, M. Rakhshandehroo, et al., Nat. Commun. 4 (2013) 2656. doi: 10.1038/ncomms3656
31. [31]
  E. Kummari, N. Alugubelly, C.Y. Hsu, et al., Plos One 10 (2015) e0135531. doi: 10.1371/journal.pone.0135531
32. [32]
  X. Sui, Y. Wang, Y.X. Du, et al., Chem. Sci. 11 (2020) 12633–12646. doi: 10.1039/D0SC03295F
33. [33]
  A.M. Sadaghiani, S.H. Verhelst, M. Bogyo, Curr. Opin. Chem. Biol. 11 (2007) 20–28. doi: 10.1016/j.cbpa.2006.11.030
34. [34]
  A. Borodovsky, H. Ovaa, W.J. Meester, et al., Chembiochem 6 (2005) 287–291. doi: 10.1002/cbic.200400236
35. [35]
  K.D. Wilkinson, T. Gan-Erdene, N. Kolli, Methods Enzymol. 399 (2005) 37–51.
36. [36]
  K.R. Love, R.K. Pandya, E. Spooner, H.L. Ploegh, ACS Chem. Biol. 4 (2009) 275–287. doi: 10.1021/cb9000348
37. [37]
  H.B. Kamadurai, J. Souphron, D.C. Scott, et al., Mol. Cell 36 (2009) 1095–1102. doi: 10.1016/j.molcel.2009.11.010
38. [38]
  M.P. Mulder, K. Witting, I. Berlin, et al., Nat. Chem. Biol. 12 (2016) 523–530. doi: 10.1038/nchembio.2084
39. [39]
  F. El Oualid, R. Merkx, R. Ekkebus, et al., Angew. Chem. Int. Ed. 49 (2010) 10149–10153. doi: 10.1002/anie.201005995
40. [40]
  G.J. Bernardes, J.M. Chalker, J.C. Errey, B.G. Davis, J. Am. Chem. Soc. 130 (2008) 5052–5053. doi: 10.1021/ja800800p
41. [41]
  J.M. Chalker, S.B. Gunnoo, O. Boutureira, et al., Chem. Sci. 2 (2011) 1666. doi: 10.1039/c1sc00185j
42. [42]
  C. Gladkova, S.L. Maslen, J.M. Skehel, D. Komander, Nature 559 (2018) 410–414. doi: 10.1038/s41586-018-0224-x
43. [43]
  D.L. Vaux, J. Silke, Nat. Rev. Mol. Cell Biol. 6 (2005) 287–297. doi: 10.1038/nrm1621
44. [44]
  K.C. Pao, M. Stanley, C. Han, et al., Nat. Chem. Biol. 12 (2016) 324–331. doi: 10.1038/nchembio.2045
45. [45]
  L. Xu, J. Fan, Y. Wang, et al., Chem. Commun. 55 (2019) 7109–7112. doi: 10.1039/C9CC03739J
46. [46]
  J. Ahel, A. Fletcher, D.B. Grabarczyk, et al., bioRxiv (2021), doi: 10.1101/2021.05.10.443411.
47. [47]
  P.D. Mabbitt, A. Loreto, M.A. Déry, et al., Nat. Chem. Biol. 16 (2020) 1227–1236. doi: 10.1038/s41589-020-0598-6
48. [48]
  D. Horn-Ghetko, D.T. Krist, J.R. Prabu, et al., Nature 590 (2021) 671–676. doi: 10.1038/s41586-021-03197-9
49. [49]
  H.B. Kamadurai, Y. Qiu, A. Deng, et al., eLife 2 (2013) e00828. doi: 10.7554/eLife.00828
50. [50]
  S. Mathur, A.J. Fletcher, E. Branigan, R.T. Hay, S. Virdee, Cell Chem. Biol. 27 (2020) 74–82. doi: 10.1016/j.chembiol.2019.11.013
51. [51]
  L. Buetow, G. Tria, S.F. Ahmed, et al., BMC Biol. 14 (2016) 76. doi: 10.1186/s12915-016-0298-6
52. [52]
  H. Dou, L. Buetow, G.J. Sibbet, K. Cameron, D.T. Huang, Nat. Struct. Mol. Biol. 20 (2013) 982–986. doi: 10.1038/nsmb.2621
53. [53]
  Y. Zhang, T. Hirota, K. Kuwata, et al., J. Am. Chem. Soc. 141 (2019) 14742–14751. doi: 10.1021/jacs.9b06820
54. [54]
  A. Plechanovová, E.G. Jaffray, M.H. Tatham, J.H. Naismith, R.T. Hay, Nature 489 (2012) 115–120. doi: 10.1038/nature11376
55. [55]
  E. Branigan, A. Plechanovová, E.G. Jaffray, J.H. Naismith, R.T. Hay, Nat. Struct. Mol. Biol. 22 (2015) 597–602. doi: 10.1038/nsmb.3052
56. [56]
  H. Dou, L. Buetow, G.J. Sibbet, K. Cameron, D.T. Huang, Nat. Struct. Mol. Biol. 19 (2012) 876–883. doi: 10.1038/nsmb.2379
57. [57]
  N.G. Brown, R. VanderLinden, E.R. Watson, et al., Cell 165 (2016) 1440–1453. doi: 10.1016/j.cell.2016.05.037
58. [58]
  K. Baek, D.T. Krist, J.R. Prabu, et al., Nature 578 (2020) 461–466. doi: 10.1038/s41586-020-2000-y
59. [59]
  G.L. Ellman, Arch. Biochem. Biophys. 82 (1959) 70–77. doi: 10.1016/0003-9861(59)90090-6
60. [60]
  M. Pan, Q. Zheng, T. Wang, et al., Nature 600 (2021) 334–338. doi: 10.1038/s41586-021-04097-8
61. [61]
  F.C. Jr. Streich, C.D. Lima, Methods Mol. Biol. 1844 (2018) 169–196.
62. [62]
  L. Cappadocia, C.D. Lima, Chem. Rev. 118 (2018) 889–918. doi: 10.1021/acs.chemrev.6b00737
63. [63]
  J. Liwocha, D.T. Krist, G.J. van der Heden van Noort, et al., Nat. Chem. Biol. 17 (2021) 272–279. doi: 10.1038/s41589-020-00696-0
64. [64]
  W. Gui, S. Shen, Z. Zhuang, J. Am. Chem. Soc. 142 (2020) 19493–19501. doi: 10.1021/jacs.9b12426
65. [65]
  Y. Wang, J. Chen, X. Hua, et al., Angew. Chem. Int. Ed. 61 (2022) e202203792.
66. [66]
  C. Grabbe, K. Husnjak, I. Dikic, Nat. Rev. Mol. Cell Biol. 12 (2011) 295–307. doi: 10.1038/nrm3099
67. [67]
  L. Huang, E. Kinnucan, G. Wang, et al., Science 286 (1999) 1321–1326. doi: 10.1126/science.286.5443.1321
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