Discovery of a potent inhibitor that suppresses glioblastoma by dual targeting of both syntenin PDZ domains

Melanoma differentiation associated gene-9 (MDA-9)/Syntenin possesses a tandem repeat of PDZ domains that exert regulatory control over cell membrane architecture through interactions with a multitude of proteins. MDA-9/Syntenin is strongly implicated in cell cycle progression, growth and metastasis of various malignant tumors, including glioblastoma multiforme (GBM), a highly aggressive and invasive tumor associated with a poor prognosis. In an effort to develop potent syntenin inhibitors capable of suppressing glioblastoma, we conducted a screening of four million compounds and found a syntenin inhibitor, Z3322068027 (SPDZi1), which selectively binds to both PDZ domains of syntenin. We have determined the crystal structure of the syntenin PDZ tandem (STNPDZ) and SPDZi1 complex at a resolution of 1.60 Å. Our findings show that SPDZi1 interacts with both the PDZ1 and PDZ2 domains of syntenin, as confirmed by the ¹ H- ¹⁵ N heteronuclear single quantum correlation (HSQC) spectrum. Treatment with SPDZi1 demonstrates a profound inhibitory effect on human GBM cell proliferation while concurrently reducing the activation of nuclear factor-kappa B (NF-κB), a downstream effector of syntenin. By treating on patient-derived glioblastoma organoids (GBOs), SPDZi1 effectively suppressed the growth of small GBOs, while co-treatment of SPDZi1 and temozolomide (TMZ) showed a synergistic suppressive effect on large established GBOs. These findings underscore the therapeutic potential of our syntenin targeting inhibitor. Furthermore, the elucidated complex structure of STNPDZ and SPDZi1, in conjunction with docking studies involving various inhibitor candidates, will assume a pivotal role in advancing structure-based drug design for addressing metastatic GBM.