Targeting an E3 ubiquitin ligase Siah1 and a cysteine protease SENP1 using SPR and DSF-based fragment screening

  • Vadim Rimsa

    Student thesis: Doctoral ThesisDoctor of Philosophy


    This dissertation presents fragment screening studies against two human proteins Siah1 and SENP1, which function in post-translational modification pathways. Siah1 is an E3 ubiquitin ligase that functions as a scaffold to transfer ubiquitin bound to an E2 ubiquitin-conjugating enzyme to a substrate as part of the ubiquitination pathway. SENP1 is a cysteine protease that catalyses two essential reactions in the SUMO pathway. It processes pre-SUMO proteins to their mature form and removes SUMO from the target proteins. Siah1 interactions with other proteins involve large surface areas, while SENP1 has a small active site, making it hard to identify ligands for these proteins. The fragment-based approach has emerged as a complementary method to high-throughput screening of finding novel small molecules. The main aim of the study was to examine whether fragment screening would identify any ligands against these targets.
    Chapter 1 introduces post-translational modifications and presents fragment-based approach used in drug discovery. Chapter 2 describes the experimental methods used. The results from fragment screening against Siah1 using SPR and DSF are reported in chapter 3. The chapter also presents the structure of Siah1 refined to 1.95 Å that displays new parts of the structure, previously missing due to the absence of reliable electron density. Chapter 4 contains results from the fragment screens against SENP1 using DSF and NMR. The crystal structure of SENP1 was determined with a number of improvements made over earlier structures.
    Besides performing fragment screening, the binding between Siah1 interacting proteins reported in the literature and Siah1 was investigated. A number of Siah1 binding partners were successfully expressed and purified as described in chapter 5. One of those, SIP showed a clear interaction with Siah1, as observed by the shift on a size exclusion column of the complex relative to the individual protein species. Siah1 was reported to collaborate with PEG3 in the regulation of ß-catenin degradation. A SCAN domain, located at the N-terminus of PEG3, was tested for binding using gel filtration chromatography and NMR, but no interaction was observed. PEG3 was used in the crystallographic studies and a structure of its SCAN domain was solved using molecular replacement and refined to 1.95 Å. The structure of PEG3-SCAN domain revealed a stable homodimer with an extensive dimerization interface.
    The structure of a zinc-dependent cytosolic carboxypeptidase from Burkholderia
    cenocepacia was determined and is reported in chapter 6. This work was a side project assessing a new refinement strategy, which involved the use of the automated protocols embedded in the PDB_REDO server. The structure revealed that carboxypeptidase is a tetramer and provides details of its active site, whose spatial conformation of residues supports the notion that the protein might function as a deglutamylase.
    Date of Award2013
    Original languageEnglish
    SupervisorBill Hunter (Supervisor)

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