Lab of Protein Homeostasis and Drug Discovery

leebyunghoon

Prof. Lee, Byung-Hoon

Assistant Professor

University of Texas Southwestern Medical Center at Dallas, PhD

Office: E4-610

Phone: +82-53-785-1730

E-mail: byung-hoon_lee@dgist.ac.kr

 

Overview

The importance of protein homeostasis has come to permeate many aspects of modern biology. Aberrant protein species and undesirable protein aggregates, if not cleared properly, compromise protein homeostasis and ultimately culminate in devastating diseases, collectively called as proteopathies.

Especially, the 26S proteasome is the principal protease for specific degradation of harmful proteins – the process known as protein quality control. The ubiquitin-proteasome system (UPS) is indeed an important drug target for human health insofar as FDA-approved proteasome inhibitors are effective in the treatment of a growing list of cancers. Deubiquitinating enzymes (DUBs), numbering over a hundred in human proteome, exclusively reverse the ubiquitination, regulate ubiquitin pool, and antagonize protein destruction (e.g. including aberrant proteins and oncoprotein). DUBs are also emerging as promising drug targets, due to their involvement in human diseases. Furthermore, DUB inhibitors may serve as specific tools for discovering novel biology in the ubiquitin-proteasome pathways.

My research primarily focused on key regulatory mechanisms occurring on the proteasome. I discovered that USP14, a major proteasome-associated deubiquitinating enzyme, acts as a critical inhibitory component on the proteasome. In addition, recently I have established a high-throughput small-molecule chemical screening platform, and as a proof-of-principle, discovered drug-like molecules targeting USP14. Highly specific USP14 inhibitors are cell-permeable and can serve as a potent enhancer of proteasome function. Through medicinal chemistry, I also have developed more potent and selective variants of USP14 inhibitors. Enhancement of proteasome activity through inhibition of USP14 may offer a strategy to reduce aberrant proteins for human health. By employing this inhibitor, I also discovered truly unanticipated supernumerary chain-specific and en bloc cleavage mechanisms governed by USP14, which occurring only on the proteasome. This is to our knowledge the first report of such a preference within the family of deubiquitinating enzymes.

This research defines proteasome and deubiquitinating enzymes in the ubiquitin-proteasome system as promising drug targets for human health. This study also highlights the significance of cellular proteome balance in normal and diseased states, and will eventually enhance our general understanding of protein homeostasis for human health.

 

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-Ubiquitin-proteasome pathway, deubiquitination reaction on the proteasome, and a specific USP14 inhibitor IU1-

 

Research Summary

Protein homeostasis through the ubiquitin-proteasome system (UPS) is critical in almost every aspect of basic and clinical biology. Our lab is particularly interested in understanding cellular protein quality control system and developing the strategies for improving proteostasis by manipulating the UPS. We will primarily investigate critical deubiquitination machinery in human pathophysiology. Our group will try to develop functional and chemical strategies to modulate the deubiquitination activities on the proteasome and at the upstream of proteasome to explore novel biological mechanisms in the ubiquitin-proteasome pathways. By developing new DUB inhibitors, we aim to define novel drug targets in protein quality control machinery and ultimately seek for potential therapeutic strategies for human health.

1. Discovery of novel deconjugation mechanisms in the ubiquitin-proteasome pathways for cell physiology

2. Investigation of novel regulatory mechanisms in ubiquitin deconjugation activities for proteasome function

3. Defining deubiquitinating enzymes as novel drug targets in oncogenesis and other human diseases by functional and chemical studies

4. Defining proteasome and deubiquitinating enzymes as novel drug targets in human longevity by combinatorial approaches of chemical and functional studies

 

leebyunghoon_F2
Understanding deubiquitination reactions on the proteasome as novel drug targets for cellular homeostasis

 

Selected Publications

  • Chen S*, Wu J*, Lu Y*, Ma YB, Lee BH, Yu Z, Quyang Q, Finley D, Kirschner M, and Mao Y. (2016) Structural basis for dynamic regulation of the human 26S proteasome. PNAS, 113(46), 12991-12996.
  • Lee BH*, Lu Y, Prado MA, Shi Y, Sun S, Elsasser S, Gygi SP, King RW*, and Finley D*. (2016) USP14 deubiquitinates proteasome-bound substrates that are ubiquitinated at multiple sites. Nature, Apr 21, 532(7599):398-401, doi: 10.1038/nature17433. (* Co-corresponding authors).
  • Shi Y*, Elsasser S*, Stocks BB*, Chen X*, Tian G, Lee BH, Shi Y, Zhang N, de Poot SA, G, Tuebing F, Sun S, Vannoy J, Tarasov SG, Engen JR, Walters KJ, and Finley D. (2016) Rpn1 provides adjacent receptor sites for substrate binding and deubiquitination by the proteasome. Science, Feb 19;351(6275). pii: aad9421. doi: 10.1126/science.aad9421.
  • Xu D, Shan B*, Lee BH*, Zhu K, Zhang T, Sun H, Liu M, Shi L, Liang W, Qian L, Xiao J, Pan L, Finley D, and Yuan J. (2015) Phosphorylation and activation of ubiquitin-specific protease-14 by Akt regulates UPS. eLife, Nov 2;4. pii: e10510. doi: 10.7554/eLife.10510, (* Co-second authors).
  • Lu Y, Lee BH, King RW, Finley D, and Kirschner M (2015) Substrate degradation by the proteasome: a single-molecule kinetic analysis. Science, 348(6231):1250834. doi: 0.1126/science.1250834.
  • Liu YP, Tsai IC, Morleo M, Oh EC, Leitch CC, Massa F, Lee BH, Parker DS, Finley D, Zaghloul NA, Franco B, Katsanis N. (2014) Ciliopathy proteins regulate paracrine signaling by modulating proteasomal degradation of mediators. J. Clin. Invest. 124(5), 2059-2070.
  • Lee BH, Finley D, and King RW. (2012) A High-Throughput Screening Method for Identification of Inhibitors of the Deubiquitinating Enzyme USP14. Curr. Protoc. Chem. Biol. 4, 311-330, John Wiley & Sons, Inc.
  • Dimova N, Hathaway NA, Lee BH, Kirkpatrick DS, Berkowitz ML, Gygi SP, Finley D, and King RW. (2012) APC/C-mediated multiple monoubiquitylation provides an alternative degradation pathway for cyclin B1. Nat. Cell Biol. 14, 168-176.
  • Lee BH*, Lee MJ*, Park S, Oh DC, Elsasser S, Chen PC, Gartner C, Dimova N, Hanna J, Gygi SP, Wilson SM, King RW, and Finley D. (2010) Enhancement of proteasome activity by a small-molecule inhibitor of USP14. Nature 467, 179-184; article; DOI: 10.1038/nature09299. (* Co-first authors).
  • Lee MJ, Lee BH, Hanna J, King RW, and Finley D. (2011) Trimming of ubiquitin chains by proteasome-associated deubiquitinating enzymes. Mol. Cell. Proteomics 10(5):R110.003871 Epub 2010 Sep 7.
  • Chen X, Lee BH, Finley D, and Walters KJ. (2010) Structure of proteasome ubiquitin receptor hRpn13 and its activation by the scaffolding protein hRpn2. Mol. Cell 38, 404-415.
  • Roelofs J, Park S, Haas W, Tian G, McAllister FE, Huo Y, Lee BH, Zhang F, Shi Y, Gygi SP, and Finley D. (2009) Chaperone-mediated pathway of proteasome regulatory particle assembly. Nature 459, 861-865.
  • Kim D, Frank CL, Dobbin MM, Tsunemoto RK, Tu W, Peng PL, Guan JS, Lee BH, Moy LY, Giusti P, Broodie N, Mazitschek R, Delalle I, Haggarty SJ, Neve RL, Lu Y, and Tsai LH. (2008) Deregulation of HDAC1 by p25/Cdk5 in neurotoxicity. Neuron 60, 803-817.
  • Lee BH, Chen W, Stippec S, and Cobb MH. (2007) Biological cross-talk between WNK1 and the transforming growth factor -Smad signaling pathway. J. Biol. Chem. 282, 17985-17996.
  • Xu BE, Stippec S, Chu PY, Lazrak A, Li XJ, Lee BH, English JM, Ortega B, Huang CL, and Cobb MH. (2005) WNK1 activates SGK1 to regulate the epithelial sodium channel. Proc. Natl. Acad. Sci. USA 102, 10315-10320.
  • Lenertz L, Lee BH, Min X, Xu BE, Wedin K, Earnest S, Goldsmith EJ, and Cobb MH. (2005) Properties of WNK1 and implications for other family members. J. Biol. Chem. 280, 26653-26658.
  • Xu BE, Lee BH, Min X, Lenertz L, Heise CJ, Stippec S, Goldsmith EJ, and Cobb MH. (2005) WNK1: analysis of protein kinase structure, downstream targets, and potential roles in hypertension. Cell Res. 15, 6-10.
  • Lee BH, Min X, Heise CJ, Xu BE, Chen S, Shu H, Luby-Phelps K, Goldsmith EJ, and Cobb MH. (2004) WNK1 phosphorylates synaptotagmin 2 and modulates its membrane binding. Mol. Cell 15, 741-751.