Developing Constrained p27 Peptides to Target the Oncogenic E3 Ubiquitin Ligase SCF-Skp2

The ubiquitin-proteasome system (UPS) maintains homeostatic levels of proteins in normal cells and controls the levels of oncogenes and tumour suppressors by tagging proteins with ubiquitin for proteasomal degradation. The UPS is regulated by sequential action of three enzymes: E1 – ubiquitin activating enzyme, E2 - ubiquitin conjugating enzyme, and E3 - ubiquitin ligase. The SCF-Skp2 complex is one of 600 E3s in the human genome, and Skp2 serves as a substrate recognition subunit. Skp2 is an oncoprotein that exerts its oncogenic functions through degradation of specific substrates. A major target of SCF-Skp2 is the cyclin-dependent kinase inhibitor p27 which positively regulates cell cycle progression. Elevated levels of Skp2 and reduced levels of p27 are common in a variety of cancers, including lymphomas and breast and prostate carcinomas. A lack of suitable binding pockets in Skp2 and the intrinsically disordered nature of p27 make this protein-protein interaction (PPI) challenging for conventional small molecule approaches. We aim to develop instead a macrocyclic peptide inhibitor for this PPI. We have designed and synthesised p27 peptides containing unnatural amino acids and successfully constrained them using ‘click’ chemistry. The dissociation constants show that the constrained peptides (CPs) have dramatically higher affinities for the Cks1-Skp2- Skp1 complex compared with the linear (unconstrained) p27 peptide. The 30 nM affinity of the tightest binding peptide is almost two orders of magnitude higher than that of the linear peptide (3 μM). We suggest that this large enhancement of affinity arises because the binding-competent form of the peptide has a tight turn-like conformation, which is very effectively constrained by the macrocyclic linker. The CPs were also shown to inhibit p27 ubiquitination in vitro. Interestingly, the CPs also inhibited the ubiquitination of two other Skp2 substrates, p21 and N-myc, to varying degrees. A number of different approaches were taken to deliver the CPs into cells and investigate their effect on p27 protein levels and on cellular proliferation. CPs were able to restore p27 levels associated with Skp2 over-expression as well as reduce proliferation of breast cancer cell line MCF-7. We additionally investigated a different route to constrain the p27 sequence by grafting it onto a loop of a small, stable protein scaffold. These grafted proteins were also able to inhibit p27 ubiquitination. Lastly, we constructed novel proteolysis-targeting proteins (polyproxins) that hijack SCF-Skp2 and direct it to drive the destruction of disease-causing proteins. We generated a library of polyproxins, combining a module that binds a cancer-associated protein, β-catenin, with a module that binds Skp2. β-catenin ubiquitination and degradation in cells was successfully demonstrated using these polyproxins

Gsk3β and Tomm20 are substrates of the SCFFbxo7/PARK15 ubiquitin ligase associated with Parkinson's disease.

Fbxo7 is a clinically relevant F-box protein, associated with both cancer and Parkinson's disease (PD). Additionally, SNPs within FBXO7 are correlated with alterations in red blood cell parameters. Point mutations within FBXO7 map within specific functional domains, including near its F-box domain and its substrate recruiting domains, suggesting that deficiencies in SCFFbxo7/PARK15 ubiquitin ligase activity are mechanistically linked to early-onset PD. To date, relatively few substrates of the ligase have been identified. These include HURP (hepatoma up-regulated protein), whose ubiquitination results in proteasome-mediated degradation, and c-IAP1 (inhibitor of apoptosis protein 1), TNF receptor-associated factor 2 (TRAF2), and NRAGE, which are not destabilized as a result of ubiquitination. None of these substrates have been linked directly to PD, nor has it been determined whether they would directly engage neuronal cell death pathways. To discover ubiquitinated substrates of SCFFbxo7 implicated more directly in PD aetiology, we conducted a high-throughput screen using protein arrays to identify new candidates. A total of 338 new targets were identified and from these we validated glycogen synthase kinase 3β (Gsk3β), which can phosphorylate α-synuclein, and translocase of outer mitochondrial membrane 20 (Tomm20), a mitochondrial translocase that, when ubiquitinated, promotes mitophagy, as SCFFbxo7 substrates both in vitro and in vivo Ubiquitin chain restriction analyses revealed that Fbxo7 modified Gsk3β using K63 linkages. Our results indicate that Fbxo7 negatively regulates Gsk3β activity, rather than its levels or localization. In addition, Fbxo7 ubiquitinated Tomm20, and its levels correlated with Fbxo7 expression, indicating a stabilizing effect. None of the PD-associated mutations in Fbxo7 impaired Tomm20 ubiquitination. Our findings demonstrate that SCFFbxo7 has an impact directly on two proteins implicated in pathological processes leading to PD.FRT was funded by a BEPE-FAPESP Fellowship (2012/09241-8). SR and HL are funded by the Biotechnology and Biological Science Research Council (BB/J007846/1). DK is funded by ERC (309756), MRC (U105192732) and the Lister Institute for Preventive Medicine. TETM is funded by the Marie Curie ITN “UPStream.”This is the final version of the article. It first appeared from Portland Press via https://doi.org/10.1042/BCJ2016038

RIP2 filament formation is required for NOD2 dependent NF-κB signalling

Binding of bacterial peptidoglycan muramyl dipeptides induces NOD2 activation and signalling via the downstream adaptor kinase RIP2. Here the authors show that RIP2 forms filaments via its CARD domain, analyse the structure of the CARD filaments and demonstrate the requirement of RIP2 polymerisation for the activation of NF-κB by NOD2