Inhibitors against Two PDZ Domains of MDA-9 Suppressed Migration of Breast Cancer Cells

Abstract

Melanoma differentiation-associated gene 9 (MDA-9) is a small adaptor protein with tandem PDZ domains that promotes tumor progression and metastasis in various human cancers. However, it is difficult to develop drug-like small molecules with high affinity due to the narrow groove of the PDZ domains of MDA-9. Herein, we identified four novel hits targeting the PDZ1 and PDZ2 domains of MDA-9, namely PI1A, PI1B, PI2A, and PI2B, using a protein-observed nuclear magnetic resonance (NMR) fragment screening method. We also solved the crystal structure of the MDA-9 PDZ1 domain in complex with PI1B and characterized the binding poses of PDZ1-PI1A and PDZ2-PI2A, guided by transferred paramagnetic relaxation enhancement. The protein–ligand interaction modes were then cross-validated by the mutagenesis of the MDA-9 PDZ domains. Competitive fluorescence polarization experiments demonstrated that PI1A and PI2A blocked the binding of natural substrates to the PDZ1 and PDZ2 domains, respectively. Furthermore, these inhibitors exhibited low cellular toxicity, but suppressed the migration of MDA-MB-231 breast carcinoma cells, which recapitulated the phenotype of MDA-9 knockdown. Our work has paved the way for the development of potent inhibitors using structure-guided fragment ligation in the future.

WITHDRAWN: Discovery of a potent inhibitor that suppresses glioblastoma by dual targeting of both syntenin PDZ domains

“…Syntenin is associated with various signaling pathways, including EGFR, VEGFR, FAK, Src, and NF-κB (Talukdar et al, 2018; Tae et al, 2017; Kegelman et al, 2015; Tang et al, 2023). The PDZ domains of syntenin interact with proteins involved in these signaling pathways and promote the migration and invasion of malignant tumors, such as breast cancer and GBM (Talukdar et al, 2018; Tae et al, 2017; Kegelman et al, 2015; Tang et al, 2023). Since SPDZi1 was expected to disrupt these interactions by binding to the PDZ domain of syntenin, we treated SPDZi1 in a GBM cell line to observe its effects.…”

“…Consequently, ongoing research aims to inhibit metastasis and migration in cancer by targeting syntenin as a therapeutic target. Recently, several inhibitors targeting the PDZ domain of syntenin have been reported (Haugaard-Kedström et al, 2021; Kegelman et al, 2017; Leblanc et al, 2020; Hoffer et al, 2023; Tang et al, 2023; Liu et al, 2018; Garcia et al, 2021). The inhibitors, with identified complex structures with syntenin, provide valuable insights for developing of improved inhibitors (Haugaard-Kedström et al, 2021; Leblanc et al, 2020; Hoffer et al, 2023; Tang et al, 2023).…”

“…Recently, several inhibitors targeting the PDZ domain of syntenin have been reported (Haugaard-Kedström et al, 2021; Kegelman et al, 2017; Leblanc et al, 2020; Hoffer et al, 2023; Tang et al, 2023; Liu et al, 2018; Garcia et al, 2021). The inhibitors, with identified complex structures with syntenin, provide valuable insights for developing of improved inhibitors (Haugaard-Kedström et al, 2021; Leblanc et al, 2020; Hoffer et al, 2023; Tang et al, 2023). Notably, only four FDA-approved drugs are available for treating GBM, a disease with a poor prognosis, and there are no drugs targeting syntenin specifically for GBM.…”