Chemical Genetics Screen for Enhancers of Rapamycin Identifies a Specific Inhibitor of an SCF Family E3 Ubiquitin Ligase

Overview

Journal Nat Biotechnol

Specialty Biotechnology

Date 2010 Jun 29

PMID 20581845

Citations 85

Authors

Mariam Aghajan

Nao Jonai

Karin Flick

Fei Fu

Manlin Luo

Xiaolu Cai

Ikram Ouni

Nathan Pierce

Xiaobo Tang

Brett Lomenick

Robert Damoiseaux

Rui Hao

Pierre M Del Moral

Rati Verma

Ying Li

Cheng Li

Kendall N Houk

Michael E Jung

Ning Zheng

Lan Huang

Raymond J Deshaies

Peter Kaiser

Jing Huang

Affiliations

Soon will be listed here.

Abstract

The target of rapamycin (TOR) plays a central role in eukaryotic cell growth control. With prevalent hyperactivation of the mammalian TOR (mTOR) pathway in human cancers, strategies to enhance TOR pathway inhibition are needed. We used a yeast-based screen to identify small-molecule enhancers of rapamycin (SMERs) and discovered an inhibitor (SMER3) of the Skp1-Cullin-F-box (SCF)(Met30) ubiquitin ligase, a member of the SCF E3-ligase family, which regulates diverse cellular processes including transcription, cell-cycle control and immune response. We show here that SMER3 inhibits SCF(Met30) in vivo and in vitro, but not the closely related SCF(Cdc4). Furthermore, we demonstrate that SMER3 diminishes binding of the F-box subunit Met30 to the SCF core complex in vivo and show evidence for SMER3 directly binding to Met30. Our results show that there is no fundamental barrier to obtaining specific inhibitors to modulate function of individual SCF complexes.

Citing Articles

The Yeast F-Box Protein Met30 Regulates Proline Utilization Independently of Transceptor Can1 Under Nutrient-Rich Conditions.

Nishimura A, Tanahashi R, Takagi H Microorganisms. 2025; 12(12.

PMID: 39770713 PMC: 11679997. DOI: 10.3390/microorganisms12122510.

Cadmium binding by the F-box domain induces p97-mediated SCF complex disassembly to activate stress response programs.

Lauinger L, Andronicos A, Flick K, Yu C, Durairaj G, Huang L Nat Commun. 2024; 15(1):3894.

PMID: 38719837 PMC: 11079001. DOI: 10.1038/s41467-024-48184-6.

Stability-Based Proteomics for Investigation of Structured RNA-Protein Interactions.

Bailey M, Martyr J, Hargrove A, Fitzgerald M Anal Chem. 2024; .

PMID: 38341805 PMC: 11316846. DOI: 10.1021/acs.analchem.3c04978.

Ubiquitin E3 Ligase FBXO9 Regulates Pluripotency by Targeting DPPA5 for Ubiquitylation and Degradation.

Swenson S, Dobish K, Peters H, Bea Winship C, Willow Hynes-Smith R, Caplan M Stem Cells. 2024; 42(4):317-328.

PMID: 38227647 PMC: 11016844. DOI: 10.1093/stmcls/sxae004.

Differential Hsp90-dependent gene expression is strain-specific and common among yeast strains.

Hung P, Liao C, Ko F, Tsai H, Leu J iScience. 2023; 26(5):106635.

PMID: 37138775 PMC: 10149407. DOI: 10.1016/j.isci.2023.106635.

References

Cloughesy T, Yoshimoto K, Nghiemphu P, Brown K, Dang J, Zhu S . Antitumor activity of rapamycin in a Phase I trial for patients with recurrent PTEN-deficient glioblastoma. PLoS Med. 2008; 5(1):e8. PMC: 2211560. DOI: 10.1371/journal.pmed.0050008. View

Kaiser P, Su N, Yen J, Ouni I, Flick K . The yeast ubiquitin ligase SCFMet30: connecting environmental and intracellular conditions to cell division. Cell Div. 2006; 1:16. PMC: 1579207. DOI: 10.1186/1747-1028-1-16. View

Shaw R, Cantley L . Ras, PI(3)K and mTOR signalling controls tumour cell growth. Nature. 2006; 441(7092):424-30. DOI: 10.1038/nature04869. View

Lomenick B, Hao R, Jonai N, Chin R, Aghajan M, Warburton S . Target identification using drug affinity responsive target stability (DARTS). Proc Natl Acad Sci U S A. 2009; 106(51):21984-9. PMC: 2789755. DOI: 10.1073/pnas.0910040106. View

Guo H, Lishko V, Herrera H, Groce A, Kubota T, Hoffman R . Therapeutic tumor-specific cell cycle block induced by methionine starvation in vivo. Cancer Res. 1993; 53(23):5676-9. View

Lee C, Inoki K, Guan K . mTOR pathway as a target in tissue hypertrophy. Annu Rev Pharmacol Toxicol. 2006; 47:443-67. DOI: 10.1146/annurev.pharmtox.47.120505.105359. View

Petroski M, Deshaies R . Function and regulation of cullin-RING ubiquitin ligases. Nat Rev Mol Cell Biol. 2005; 6(1):9-20. DOI: 10.1038/nrm1547. View

Wullschleger S, Loewith R, Hall M . TOR signaling in growth and metabolism. Cell. 2006; 124(3):471-84. DOI: 10.1016/j.cell.2006.01.016. View

Dorrello N, Peschiaroli A, Guardavaccaro D, Colburn N, Sherman N, Pagano M . S6K1- and betaTRCP-mediated degradation of PDCD4 promotes protein translation and cell growth. Science. 2006; 314(5798):467-71. DOI: 10.1126/science.1130276. View

10.

HALPERN B, Clark B, Hardy D, HALPERN R, Smith R . The effect of replacement of methionine by homocystine on survival of malignant and normal adult mammalian cells in culture. Proc Natl Acad Sci U S A. 1974; 71(4):1133-6. PMC: 388177. DOI: 10.1073/pnas.71.4.1133. View

11.

Chen Q, Xie W, Kuhn D, Voorhees P, Lopez-Girona A, Mendy D . Targeting the p27 E3 ligase SCF(Skp2) results in p27- and Skp2-mediated cell-cycle arrest and activation of autophagy. Blood. 2008; 111(9):4690-9. PMC: 2343599. DOI: 10.1182/blood-2007-09-112904. View

12.

Harrison D, Strong R, Sharp Z, Nelson J, Astle C, Flurkey K . Rapamycin fed late in life extends lifespan in genetically heterogeneous mice. Nature. 2009; 460(7253):392-5. PMC: 2786175. DOI: 10.1038/nature08221. View

13.

Huang J, Zhu H, Haggarty S, Spring D, Hwang H, Jin F . Finding new components of the target of rapamycin (TOR) signaling network through chemical genetics and proteome chips. Proc Natl Acad Sci U S A. 2004; 101(47):16594-9. PMC: 527135. DOI: 10.1073/pnas.0407117101. View

14.

Knight Z, Shokat K . Features of selective kinase inhibitors. Chem Biol. 2005; 12(6):621-37. DOI: 10.1016/j.chembiol.2005.04.011. View

15.

Nakajima H, Fujiwara H, Furuichi Y, Tanaka K, Shimbara N . A novel small-molecule inhibitor of NF-kappaB signaling. Biochem Biophys Res Commun. 2008; 368(4):1007-13. DOI: 10.1016/j.bbrc.2008.01.166. View

16.

Soucy T, Smith P, Milhollen M, Berger A, Gavin J, Adhikari S . An inhibitor of NEDD8-activating enzyme as a new approach to treat cancer. Nature. 2009; 458(7239):732-6. DOI: 10.1038/nature07884. View

17.

Guertin D, Sabatini D . Defining the role of mTOR in cancer. Cancer Cell. 2007; 12(1):9-22. DOI: 10.1016/j.ccr.2007.05.008. View

18.

Sawyers C . Imatinib GIST keeps finding new indications: successful treatment of dermatofibrosarcoma protuberans by targeted inhibition of the platelet-derived growth factor receptor. J Clin Oncol. 2002; 20(17):3568-9. DOI: 10.1200/JCO.2002.20.17.3568. View

19.

Niesen F, Berglund H, Vedadi M . The use of differential scanning fluorimetry to detect ligand interactions that promote protein stability. Nat Protoc. 2007; 2(9):2212-21. DOI: 10.1038/nprot.2007.321. View

20.

Nalepa G, Rolfe M, Harper J . Drug discovery in the ubiquitin-proteasome system. Nat Rev Drug Discov. 2006; 5(7):596-613. DOI: 10.1038/nrd2056. View