Author ORCID Identifier
Date of Award
Department or Program
Biochemistry and Cell Biology
Dale F. Mierke
The NF-κB pathway is important for cell survival and proliferation, inflammation, and innate immunity, and its dysregulation is a common theme in many cancers, autoimmune disorders, and other disease states. The protein-protein interaction between the scaffolding protein NEMO and the kinase IKK in the NF-κB pathway represents a compelling target for selective NF-κB inhibition because it occurs only in the canonical branch of the NF-κB pathway. Disruption of the NEMO:IKK interaction has been established for decades in the literature as a safe and effective way to selectively inhibit overactivation of the canonical branch of the NF-κB pathway. The benchmark in the literature for disruption of the NEMO:IKK interaction is a peptide derived from the NEMO-binding domain of IKK, also called the NBD peptide. Various obstacles have thus far prevented the NBD peptide or other inhibitors of the NEMO:IKK interaction from entering the clinic. The complexity of the pathway and its crosstalk with other cellular processes present a challenge for therapeutic intervention, and biochemical and biophysical assays are made difficult by the poor solution behavior of the proteins involved.The following manuscript reports my contribution to the structure-based drug discovery campaign to inhibit the NEMO:IKK interaction by binding to NEMO in its IKK-binding domain. My work encompasses the effort to characterize the binding of previously and newly discovered molecules and various NEMO constructs via biochemical and structural methods to enable inhibitor validation by X-ray crystallography and NMR. The results of my work include a high-resolution cocrystal structure of NEMO in complex with a small molecule fragment and led to the discovery of a novel peptide sequence that binds NEMO with similar affinity to NEMO as the NBD peptide.
Kennedy, Amy, "Structure-based targeting of the NEMO:IKK interaction for canonical NF-κB inhibition" (2024). Dartmouth College Ph.D Dissertations. 218.
Available for download on Saturday, November 22, 2025