8HCK

NMR fragment-based screening against the two PDZ do-mains of MDA-9

8HCK の概要

• エントリーDOI: 10.2210/pdb8hck/pdb
• 分子名称: Syntenin-1, 4-BUTYL-1,2-DIPHENYL-PYRAZOLIDINE-3,5-DIONE, SULFATE ION, ... (5 entities in total)
• 機能のキーワード: e.g.mda-9, pdzdomain, inhibitor, therapeutic target, cell invasion
• 由来する生物種: Homo sapiens (human)
• タンパク質・核酸の鎖数: 1
• 化学式量合計: 9635.07

構造登録者

Tang, H. (登録日: 2022-11-01, 公開日: 2023-11-08, 最終更新日: 2024-11-20)

主引用文献

Tang, H.,Wang, L.,Li, S.,Wei, X.,Lv, M.,Zhong, F.,Liu, Y.,Liu, J.,Fu, B.,Zhu, Q.,Wang, D.,Liu, J.,Ruan, K.,Gao, J.,Xu, W.
Inhibitors against Two PDZ Domains of MDA-9 Suppressed Migration of Breast Cancer Cells.
Int J Mol Sci, 24:-, 2023

PubMed 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.

PubMed: 36834839
DOI: 10.3390/ijms24043431

実験手法

X-RAY DIFFRACTION (2 Å)