Purpose(s)
The Ubiquitin-Proteasome System (UPS) is vital in regulating a plethora of aspects of protein function.  Its regulatory mechanism is involved in many, if not all cellular processes. The UPS consists of three main enzymes: 2 E1 activating, ~ 38 E2  conjugating and over 600 E3 ligase enzymes.
Abnormal activity of these enzymes has been associated with diseases such as cancer,  neurodegenerative diseases, muscle dystrophy,  and more. Drugs such as Bortezomib, show that inhibiting parts of the UPS can be effective therapeutic treatments.
Inhibitory molecules have been developed for both E1 and E3 enzymes, however, there is a lack of these molecules targeting E2 enzymes specifically. This research attempts to rationally design linked-domain protein inhibitors of E2- Â conjugating enzymes, specifically Ube2D. Our inhibitor designs are based on mechanistic and structural knowledge of ubiquitin transfer. By developing Ube2D inhibitors, we seek to evaluate whether the E2-conjugating enzyme is a potential therapeutic target in treatments for various diseases such as cancer.
Method(s)
IAP2 and UHRF1 are both E3-ligase binding partners of Ube2D that are able to auto-ubiquitinate.  If Ube2D is successfully inhibited, we should observe decreased levels of both auto-ubiquitinated UHRF1  and IAP2. To test this, we performed ubiquitylation assays in the presence of either IAP2 or UHRF1,  fluorescently labelled ubiquitin and one of our 3  inhibitors ranging in concentrations from 62 µM to 38  nM. APC/C CDC20 inhibition assays were also performed in the presence of different E2 enzymes and Ubox-Ubl to investigate inhibitor specificity. To determine the binding affinity of each of our inhibitors, we performed isothermal calorimetry experiments and utilized the saturation curve to determine their Kd values. To elucidate the structure of the UUD1.1~Ube2D1 complex we individually purified Ube2D1 and UUD1.1 and ran them over a  size exclusion column. The complex was then screened against The Berkeley Screen of crystallization conditions. We are currently optimizing our crystallization conditions.
Result(s)
(Please see the poster)
Conclusion(s)
We successfully designed, expressed and tested 3 novel Ube2D inhibitors
Kd values were determined at 5 nM, 300 nM and 3 µM for UUD1.1, UU and RU respectively
IAP2 and UHRF1 inhibition assays corroborated the Kd values and showed that UUD1.1 interfered with E3 auto- ubiquitination the most
UHRF1 inhibition assays show UUD1.1 (linked-domain) has a higher efficacy compared to UbvD1.1 (single- domain) inhibitor.
UbvD1.1 is unable to prevent E2 auto-ubiquitination, whereas UUD1.1 shows robust E2 auto-ubiquitination inhibition.
Future Work
Yeast-Two Hybrid Assays to determine inhibitor specificity.
Proteomics to explore the potential of a ubiquitinome reprogramming mechanism
Test K48-linked poly-Ub levels in HeLa cells in the presence of UUD1.1 and UU WT
Test inhibitors in different cancer cell lines