Structure-Guided Design of Peptides As Tools to Probe the Protein-Protein Interaction Between Cullin-2 and Elongin BC Substrate Adaptor in Cullin RING E3 Ubiquitin Ligases

Overview

Journal ChemMedChem

Specialties Chemistry
Pharmacology

Date 2017 Aug 5

PMID 28776949

Citations 6

Authors

Teresa A F Cardote

Alessio Ciulli

Affiliations

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Abstract

Cullin RING E3 ubiquitin ligases (CRLs) are large dynamic multi-subunit complexes that control the fate of many proteins in cells. CRLs are attractive drug targets for the development of small-molecule inhibitors and chemical inducers of protein degradation. Herein we describe a structure-guided biophysical approach to probe the protein-protein interaction (PPI) between the Cullin-2 scaffold protein and the adaptor subunits Elongin BC within the context of the von Hippel-Lindau complex (CRL2 ) using peptides. Two peptides were shown to bind at the targeted binding site on Elongin C, named the "EloC site", with micromolar dissociation constants, providing a starting point for future optimization. Our results suggest ligandability of the EloC binding site to short linear peptides, unveiling the opportunity and challenges to develop small molecules that have the potential to target selectively the Cul2-adaptor PPI within CRLs.

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References

Vranken W, Boucher W, Stevens T, Fogh R, Pajon A, Llinas M . The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins. 2005; 59(4):687-96. DOI: 10.1002/prot.20449. View

Fischer E, Park E, Eck M, Thoma N . SPLINTS: small-molecule protein ligand interface stabilizers. Curr Opin Struct Biol. 2016; 37:115-22. PMC: 4834252. DOI: 10.1016/j.sbi.2016.01.004. View

Williamson M . Using chemical shift perturbation to characterise ligand binding. Prog Nucl Magn Reson Spectrosc. 2013; 73:1-16. DOI: 10.1016/j.pnmrs.2013.02.001. View

Chen Z, Sui J, Zhang F, Zhang C . Cullin family proteins and tumorigenesis: genetic association and molecular mechanisms. J Cancer. 2015; 6(3):233-42. PMC: 4317758. DOI: 10.7150/jca.11076. View

Van Molle I, Thomann A, Buckley D, So E, Lang S, Crews C . Dissecting fragment-based lead discovery at the von Hippel-Lindau protein:hypoxia inducible factor 1α protein-protein interface. Chem Biol. 2012; 19(10):1300-12. PMC: 3551621. DOI: 10.1016/j.chembiol.2012.08.015. View

Cardote T, Ciulli A . Cyclic and Macrocyclic Peptides as Chemical Tools To Recognise Protein Surfaces and Probe Protein-Protein Interactions. ChemMedChem. 2015; 11(8):787-94. PMC: 4848765. DOI: 10.1002/cmdc.201500450. View

Chan C, Morrow J, Li C, Gao Y, Jin G, Moten A . Pharmacological inactivation of Skp2 SCF ubiquitin ligase restricts cancer stem cell traits and cancer progression. Cell. 2013; 154(3):556-68. PMC: 3845452. DOI: 10.1016/j.cell.2013.06.048. View

Gadd M, Testa A, Lucas X, Chan K, Chen W, Lamont D . Structural basis of PROTAC cooperative recognition for selective protein degradation. Nat Chem Biol. 2017; 13(5):514-521. PMC: 5392356. DOI: 10.1038/nchembio.2329. View

Arkin M, Tang Y, Wells J . Small-molecule inhibitors of protein-protein interactions: progressing toward the reality. Chem Biol. 2014; 21(9):1102-14. PMC: 4179228. DOI: 10.1016/j.chembiol.2014.09.001. View

10.

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

11.

Scott D, Bayly A, Abell C, Skidmore J . Small molecules, big targets: drug discovery faces the protein-protein interaction challenge. Nat Rev Drug Discov. 2016; 15(8):533-50. DOI: 10.1038/nrd.2016.29. View

12.

Lai A, Crews C . Induced protein degradation: an emerging drug discovery paradigm. Nat Rev Drug Discov. 2016; 16(2):101-114. PMC: 5684876. DOI: 10.1038/nrd.2016.211. View

13.

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

14.

Nguyen H, Yang H, Fribourgh J, Wolfe L, Xiong Y . Insights into Cullin-RING E3 ubiquitin ligase recruitment: structure of the VHL-EloBC-Cul2 complex. Structure. 2015; 23(3):441-449. PMC: 4351159. DOI: 10.1016/j.str.2014.12.014. View

15.

Cardote T, Gadd M, Ciulli A . Crystal Structure of the Cul2-Rbx1-EloBC-VHL Ubiquitin Ligase Complex. Structure. 2017; 25(6):901-911.e3. PMC: 5462531. DOI: 10.1016/j.str.2017.04.009. View

16.

Galdeano C, Gadd M, Soares P, Scaffidi S, Van Molle I, Birced I . 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. 2014; 57(20):8657-63. PMC: 4207132. DOI: 10.1021/jm5011258. View

17.

Knauth K, Cartwright E, Freund S, Bycroft M, Buchberger A . VHL mutations linked to type 2C von Hippel-Lindau disease cause extensive structural perturbations in pVHL. J Biol Chem. 2009; 284(16):10514-22. PMC: 2667738. DOI: 10.1074/jbc.M809056200. View

18.

Morreale F, Walden H . Types of Ubiquitin Ligases. Cell. 2016; 165(1):248-248.e1. DOI: 10.1016/j.cell.2016.03.003. View

19.

Cardote T, Ciulli A . Structure-Guided Design of Peptides as Tools to Probe the Protein-Protein Interaction between Cullin-2 and Elongin BC Substrate Adaptor in Cullin RING E3 Ubiquitin Ligases. ChemMedChem. 2017; 12(18):1491-1496. PMC: 5639367. DOI: 10.1002/cmdc.201700359. View

20.

Bulatov E, Ciulli A . Targeting Cullin-RING E3 ubiquitin ligases for drug discovery: structure, assembly and small-molecule modulation. Biochem J. 2015; 467(3):365-86. PMC: 4403949. DOI: 10.1042/BJ20141450. View