Cells require specific molecular entities to regulate biological processes, which are often out of balance in diseases. Once these entities are identified, their activities may be modulated by specific ligands. DPP4 protein is an example of a target to successfully treat type II diabetes by small molecule ligands . Other members of the DPP4 family are similarly interesting. DPP8 and DPP9, are active serine proteases located inside cells. They are relevant in immune response and cancer . It is crucial to understand their structures, enzymatic mechanisms and interactions to enable structure-based drug development. DPP8 and DPP9 activity can be modulated by inhibitors like SLRFLYEG, 1G244, and Val-BoroPro. SLRFLYEG is a specific peptidic DPP8 and DPP9 inhibitor with allosteric properties. This inhibitor was designed using a segment of SUMO1. 1G244 is a strong specific competitive inhibitor of DPP8 and DPP9. Val-BoroPro is a non-specific covalent inhibitor of DPP4, DPP8 and DPP9. Regarding binding partners, SUMO1 has been described to form complex with either DPP8 or DPP9 during pulldown experiments using SUMO1-tagged beads. While the complexes are not stable in solution this binding may regulate important signaling in cells.
We hereby reveal DPP8 and DPP9 molecular structures and substrate binding features. Moreover, we clarify how structural differences in inhibitor binding lead to differences in potency and binding mechanisms. DPP8 and DPP9 are structurally related to DPP4, with a conserved α-hydrolase domain and β-propeller domain. However, the mechanism underlying the enzymatic activity differs significantly. We observed a disorder-order transition of a 26 aa segment upon substrate binding. This segment partially folds into an α-helix, which is required to fix the incoming substrate, allowing enzyme activity . Furthermore, we characterize the SUMO1-DPP9 complex using protein-protein interaction assays. We observed a stable complex between DPP9 and oligomeric forms of SUMO1. Therefore, a bis-sumoylated substrate might be the minimal requirement for interaction in a physiological context. The determination of DPP8 and DPP9 crystallographic structures as well as their interaction with SUMO1 can be of paramount relevance in immunological regulation or drug design when treating diseases like cancer.