Structure, substrate identification and drug discovery for ubiquitin ligases involved in human cancer

Project Overview

Substrate degradation by Cullin RING E3 ligases

The human genome encodes for over 500 E3 ubiquitin ligases that bind to specific substrate proteins to tag them with poly or mono-ubiquitin as a mark for protein degradation or other change in activity or localization. This process is fundamental to most biology and is frequently disrupted in human cancers and other genetic diseases. Work to identify the substrate proteins and to map their recognition motifs for specific E3 ubiquitin ligases is critical to understand these disease mechanisms. E3 ubiquitin ligases have also emerged as one of the most exciting new areas for drug discovery.  Small molecule inhibitors blocking the substrate-binding sites of E3 ligases can help to stabilise tumour suppressor proteins. Conversely, ‘PROTAC’ (proteolysis targeting chimera) drug development aims to use small molecule fusions to recruit specific drug targets (e.g. oncogenes) to E3 ligases for degradation. This can result in a far stronger and more rubust drug effect than traditional inhibitors.

This studentship will focus on Cullin-RING E3 ligases, with special focus on the BTB-Kelch family which represents the largest group of druggable E3 ubiquitin ligases. These proteins have critical roles in the control of cancer and cellular division, blood pressure, the anti-oxidant response, muscle development and neurodegeneration. The student will use mass spectrometry-based proteomics and peptide array approaches to characterise the substrates of novel E3 ligases and validate these interactions in cell based and biophysical assays. E3 ligases of interest will be screened against small molecule drug libraries and assays developed to conduct these screens.  The structural basis for substrate and drug binding interactions will be determined by X-ray crystallography. Where appropriate, E3 ligases will be investigated in cancer models, such as medulloblastoma cells, including the exploration of drug and radiotherapy opportunities.

Training Opportunities

The student will learn extensively about protein structure and cellular function with a special focus on ubiquitylation and its importance in drug discovery. Training will be given in all aspects of molecular biology and cell culture from routine cloning, site-directed mutagenesis and CRISPR/Cas9 editing to protein expression and purification in vitro and in human cell lines. Proteins will be analysed using bioinformatic, biochemical and biophysical techniques including peptide array, fluorescence plate reader assays, BIAcore kinetic assays, calorimetry and mass spectrometry. As part of the structural genomics consortium (SGC) the student will also make use of state of art facilities for protein crystallisation, X-ray diffraction and structure determination. The student will also benefit from extensive collaborations with both academia and industry. In addition, through joint supervision in the Department of Oncology the student will have access to many cancer models and further expertise in cancer cell biology and radiation treatment.

Theme

Protein Science & Structural Biology and Cancer Biology

Admissions

Project reference number: 1006

Funding and admissions information

Supervisors

Name Department Institution Country Email
Dr Alex Bullock Structural Genomics Consortium Oxford University, Old Road Campus Research Building GBR alex.bullock@sgc.ox.ac.uk
Vincenzo D'Angiolella Oncology University of Oxford GBR vincenzo.dangiolella@oncology.ox.ac.uk

D'Angiolella V, Donato V, Vijayakumar S, Saraf A, Florens L, Washburn MP, Dynlacht B, Pagano M. 2010. SCF(Cyclin F) controls centrosome homeostasis and mitotic fidelity through CP110 degradation. Nature, 466 (7302), pp. 138-42. Read abstract | Read more

Generally, F-box proteins are the substrate recognition subunits of SCF (Skp1-Cul1-F-box protein) ubiquitin ligase complexes, which mediate the timely proteolysis of important eukaryotic regulatory proteins. Mammalian genomes encode roughly 70 F-box proteins, but only a handful have established functions. The F-box protein family obtained its name from Cyclin F (also called Fbxo1), in which the F-box motif (the approximately 40-amino-acid domain required for binding to Skp1) was first described. Cyclin F, which is encoded by an essential gene, also contains a cyclin box domain, but in contrast to most cyclins, it does not bind or activate any cyclin-dependent kinases (CDKs). However, like other cyclins, Cyclin F oscillates during the cell cycle, with protein levels peaking in G2. Despite its essential nature and status as the founding member of the F-box protein family, Cyclin F remains an orphan protein, whose functions are unknown. Starting from an unbiased screen, we identified CP110, a protein that is essential for centrosome duplication, as an interactor and substrate of Cyclin F. Using a mode of substrate binding distinct from other F-box protein-substrate pairs, CP110 and Cyclin F physically associate on the centrioles during the G2 phase of the cell cycle, and CP110 is ubiquitylated by the SCF(Cyclin F) ubiquitin ligase complex, leading to its degradation. siRNA-mediated depletion of Cyclin F in G2 induces centrosomal and mitotic abnormalities, such as multipolar spindles and asymmetric, bipolar spindles with lagging chromosomes. These phenotypes were reverted by co-silencing CP110 and were recapitulated by expressing a stable mutant of CP110 that cannot bind Cyclin F. Finally, expression of a stable CP110 mutant in cultured cells also promotes the formation of micronuclei, a hallmark of chromosome instability. We propose that SCF(Cyclin F)-mediated degradation of CP110 is required for the fidelity of mitosis and genome integrity. Hide abstract

Raducu M, Fung E, Serres S, Infante P, Barberis A, Fischer R, Bristow C, Thézénas ML, Finta C, Christianson JC, Buffa FM, Kessler BM, Sibson NR, Di Marcotullio L, Toftgård R, D'Angiolella V. 2016. SCF (Fbxl17) ubiquitylation of Sufu regulates Hedgehog signaling and medulloblastoma development. EMBO J., 35 (13), pp. 1400-16. Read abstract | Read more

Skp1-Cul1-F-box protein (SCF) ubiquitin ligases direct cell survival decisions by controlling protein ubiquitylation and degradation. Sufu (Suppressor of fused) is a central regulator of Hh (Hedgehog) signaling and acts as a tumor suppressor by maintaining the Gli (Glioma-associated oncogene homolog) transcription factors inactive. Although Sufu has a pivotal role in Hh signaling, the players involved in controlling Sufu levels and their role in tumor growth are unknown. Here, we show that Fbxl17 (F-box and leucine-rich repeat protein 17) targets Sufu for proteolysis in the nucleus. The ubiquitylation of Sufu, mediated by Fbxl17, allows the release of Gli1 from Sufu for proper Hh signal transduction. Depletion of Fbxl17 leads to defective Hh signaling associated with an impaired cancer cell proliferation and medulloblastoma tumor growth. Furthermore, we identify a mutation in Sufu, occurring in medulloblastoma of patients with Gorlin syndrome, which increases Sufu turnover through Fbxl17-mediated polyubiquitylation and leads to a sustained Hh signaling activation. In summary, our findings reveal Fbxl17 as a novel regulator of Hh pathway and highlight the perturbation of the Fbxl17-Sufu axis in the pathogenesis of medulloblastoma. Hide abstract

Mavrommati I, Faedda R, Galasso G, Li J, Burdova K, Fischer R, Kessler BM, Carrero ZI, Guardavaccaro D, Pagano M, D'Angiolella V. 2018. β-TrCP- and Casein Kinase II-Mediated Degradation of Cyclin F Controls Timely Mitotic Progression. Cell Rep, 24 (13), pp. 3404-3412. Read abstract | Read more

Orderly progressions of events in the cell division cycle are necessary to ensure the replication of DNA and cell division. Checkpoint systems allow the accurate execution of each cell-cycle phase. The precise regulation of the levels of cyclin proteins is fundamental to coordinate cell division with checkpoints, avoiding genome instability. Cyclin F has important functions in regulating the cell cycle during the G2 checkpoint; however, the mechanisms underlying the regulation of cyclin F are poorly understood. Here, we observe that cyclin F is regulated by proteolysis through β-TrCP. β-TrCP recognizes cyclin F through a non-canonical degron site (TSGXXS) after its phosphorylation by casein kinase II. The degradation of cyclin F mediated by β-TrCP occurs at the G2/M transition. This event is required to promote mitotic progression and favors the activation of a transcriptional program required for mitosis. Hide abstract

Canning P, Cooper CD, Krojer T, Murray JW, Pike AC, Chaikuad A, Keates T, Thangaratnarajah C, Hojzan V, Ayinampudi V, Marsden BD, Gileadi O, Knapp S, von Delft F, Bullock AN. 2013. Structural basis for Cul3 protein assembly with the BTB-Kelch family of E3 ubiquitin ligases. J. Biol. Chem., 288 (11), pp. 7803-14. Read abstract | Read more

Cullin-RING ligases are multisubunit E3 ubiquitin ligases that recruit substrate-specific adaptors to catalyze protein ubiquitylation. Cul3-based Cullin-RING ligases are uniquely associated with BTB adaptors that incorporate homodimerization, Cul3 assembly, and substrate recognition into a single multidomain protein, of which the best known are BTB-BACK-Kelch domain proteins, including KEAP1. Cul3 assembly requires a BTB protein "3-box" motif, analogous to the F-box and SOCS box motifs of other Cullin-based E3s. To define the molecular basis for this assembly and the overall architecture of the E3, we determined the crystal structures of the BTB-BACK domains of KLHL11 both alone and in complex with Cul3, along with the Kelch domain structures of KLHL2 (Mayven), KLHL7, KLHL12, and KBTBD5. We show that Cul3 interaction is dependent on a unique N-terminal extension sequence that packs against the 3-box in a hydrophobic groove centrally located between the BTB and BACK domains. Deletion of this N-terminal region results in a 30-fold loss in affinity. The presented data offer a model for the quaternary assembly of this E3 class that supports the bivalent capture of Nrf2 and reveals potential new sites for E3 inhibitor design. Hide abstract

Canning P, Bullock AN. 2014. New strategies to inhibit KEAP1 and the Cul3-based E3 ubiquitin ligases. Biochem. Soc. Trans., 42 (1), pp. 103-7. Read abstract | Read more

E3 ubiquitin ligases that direct substrate proteins to the ubiquitin-proteasome system are promising, though largely unexplored drug targets both because of their function and their remarkable specificity. CRLs [Cullin-RING (really interesting new gene) ligases] are the largest group of E3 ligases and function as modular multisubunit complexes constructed around a Cullin-family scaffold protein. The Cul3-based CRLs uniquely assemble with BTB (broad complex/tramtrack/bric-à-brac) proteins that also homodimerize and perform the role of both the Cullin adapter and the substrate-recognition component of the E3. The most prominent member is the BTB-BACK (BTB and C-terminal Kelch)-Kelch protein KEAP1 (Kelch-like ECH-associated protein 1), a master regulator of the oxidative stress response and a potential drug target for common conditions such as diabetes, Alzheimer's disease and Parkinson's disease. Structural characterization of BTB-Cul3 complexes has revealed a number of critical assembly mechanisms, including the binding of an N-terminal Cullin extension to a bihelical '3-box' at the C-terminus of the BTB domain. Improved understanding of the structure of these complexes should contribute significantly to the effort to develop novel therapeutics targeted to CRL3-regulated pathways. Hide abstract

Schumacher FR, Sorrell FJ, Alessi DR, Bullock AN, Kurz T. 2014. Structural and biochemical characterization of the KLHL3-WNK kinase interaction important in blood pressure regulation. Biochem. J., 460 (2), pp. 237-46. Read abstract | Read more

WNK1 [with no lysine (K)] and WNK4 regulate blood pressure by controlling the activity of ion co-transporters in the kidney. Groundbreaking work has revealed that the ubiquitylation and hence levels of WNK isoforms are controlled by a Cullin-RING E3 ubiquitin ligase complex (CRL3KLHL3) that utilizes CUL3 (Cullin3) and its substrate adaptor, KLHL3 (Kelch-like protein 3). Loss-of-function mutations in either CUL3 or KLHL3 cause the hereditary high blood pressure disease Gordon's syndrome by stabilizing WNK isoforms. KLHL3 binds to a highly conserved degron motif located within the C-terminal non-catalytic domain of WNK isoforms. This interaction is essential for ubiquitylation by CRL3KLHL3 and disease-causing mutations in WNK4 and KLHL3 exert their effects on blood pressure by disrupting this interaction. In the present study, we report on the crystal structure of the KLHL3 Kelch domain in complex with the WNK4 degron motif. This reveals an intricate web of interactions between conserved residues on the surface of the Kelch domain β-propeller and the WNK4 degron motif. Importantly, many of the disease-causing mutations inhibit binding by disrupting critical interface contacts. We also present the structure of the WNK4 degron motif in complex with KLHL2 that has also been reported to bind WNK4. This confirms that KLHL2 interacts with WNK kinases in a similar manner to KLHL3, but strikingly different to how another KLHL protein, KEAP1 (Kelch-like enoyl-CoA hydratase-associated protein 1), binds to its substrate NRF2 (nuclear factor-erythroid 2-related factor 2). The present study provides further insights into how Kelch-like adaptor proteins recognize their substrates and provides a structural basis for how mutations in WNK4 and KLHL3 lead to hypertension. Hide abstract

Zhang T, Kwiatkowski N, Olson CM, Dixon-Clarke SE, Abraham BJ, Greifenberg AK, Ficarro SB, Elkins JM, Liang Y, Hannett NM, Manz T, Hao M, Bartkowiak B, Greenleaf AL, Marto JA, Geyer M, Bullock AN, Young RA, Gray NS. 2016. Covalent targeting of remote cysteine residues to develop CDK12 and CDK13 inhibitors. Nat. Chem. Biol., 12 (10), pp. 876-84. Read abstract | Read more

Cyclin-dependent kinases 12 and 13 (CDK12 and CDK13) play critical roles in the regulation of gene transcription. However, the absence of CDK12 and CDK13 inhibitors has hindered the ability to investigate the consequences of their inhibition in healthy cells and cancer cells. Here we describe the rational design of a first-in-class CDK12 and CDK13 covalent inhibitor, THZ531. Co-crystallization of THZ531 with CDK12-cyclin K indicates that THZ531 irreversibly targets a cysteine located outside the kinase domain. THZ531 causes a loss of gene expression with concurrent loss of elongating and hyperphosphorylated RNA polymerase II. In particular, THZ531 substantially decreases the expression of DNA damage response genes and key super-enhancer-associated transcription factor genes. Coincident with transcriptional perturbation, THZ531 dramatically induced apoptotic cell death. Small molecules capable of specifically targeting CDK12 and CDK13 may thus help identify cancer subtypes that are particularly dependent on their kinase activities. Hide abstract