A druggable pocket on PSMD10^Gankyrin that can accommodate an interface peptide and doxorubicin

PSMD10^Gankyrin, a proteasomal chaperone is also an oncoprotein. Overexpression of PSMD10^Gankyrin is associated with poor prognosis and survival in many cancers. Therefore, PSMD10^Gankyrin is a sought-after drug target in many hard-to-treat cancers. However, its surface appears flat and undruggable. Here, we build on our earlier discovery of a common hot spot region that defined the interface of multiple interacting partners of PSMD10^Gankyrin to expose vulnerable spots for a peptide and a small molecule inhibitor.

High throughput virtual screening was used to screen compounds against PSMD10^Gankyrin. Interaction of PSMD10^Gankyrin with the drug or protein (CLIC1) or peptide was studied using any one or more of these techniques; Microscale Thermophoresis, limited trypsinolysis, SPR and ITC. Cytotoxic effect of doxorubicin was evaluated using MTT assay.

We identified doxorubicin as the first-generation small molecule inhibitor of PSMD10^Gankyrin. K116 and to a lesser extent R41 on PSMD10^Gankyrin contribute to the bulk of binding energy for the peptide EEVD, CLIC1 and doxorubicin. We further demonstrate that PSMD10^Gankyrin is an intended target for doxorubicin in cells.

Drug design against protein interactions in general and PSMD10^Gankyrin in particular, remains a challenge. We provide consolidated biophysical evidence for the use of a shared interface motif EEVD as a possible inhibitor of interaction network in cancers driven by PSMD10^Gankyrin. We identify a chemical scaffold for designing novel inhibitors of PSMD10^Gankyrin. These findings will impact the field of protein interactions in the context of disease biology/drug discovery.