Structure and decoy-mediated inhibition of the SOX18/Prox1-DNA interaction

• Published in: Nucleic acids research Vol. 44; no. 8; pp. 3922 - 3935
• Main Authors: Klaus, Miriam, Prokoph, Nina, Girbig, Mathias, Wang, Xuecong, Huang, Yong-Heng, Srivastava, Yogesh, Hou, Linlin, Narasimhan, Kamesh, Kolatkar, Prasanna R, Francois, Mathias, Jauch, Ralf
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 05.05.2016
• Subjects: Animals; Cercopithecus aethiops; COS Cells; DNA - chemistry; DNA - metabolism; Gene Expression Regulation; Homeodomain Proteins - genetics; Mice; Nucleic Acid Conformation; Oligonucleotides; SOX Transcription Factors - chemistry; SOX Transcription Factors - metabolism; SOXF Transcription Factors - antagonists & inhibitors; SOXF Transcription Factors - chemistry; SOXF Transcription Factors - metabolism; Structural Biology; Transcription, Genetic; Tumor Suppressor Proteins - genetics
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkw130

The transcription factor (TF) SOX18 drives lymphatic vessel development in both embryogenesis and tumour-induced neo-lymphangiogenesis. Genetic disruption of Sox18 in a mouse model protects from tumour metastasis and established the SOX18 protein as a molecular target. Here, we report the crystal structure of the SOX18 DNA binding high-mobility group (HMG) box bound to a DNA element regulating Prox1 transcription. The crystals diffracted to 1.75Å presenting the highest resolution structure of a SOX/DNA complex presently available revealing water structure, structural adjustments at the DNA contact interface and non-canonical conformations of the DNA backbone. To explore alternatives to challenging small molecule approaches for targeting the DNA-binding activity of SOX18, we designed a set of five decoys based on modified Prox1-DNA. Four decoys potently inhibited DNA binding of SOX18 in vitro and did not interact with non-SOX TFs. Serum stability, nuclease resistance and thermal denaturation assays demonstrated that a decoy circularized with a hexaethylene glycol linker and terminal phosphorothioate modifications is most stable. This SOX decoy also interfered with the expression of a luciferase reporter under control of a SOX18-dependent VCAM1 promoter in COS7 cells. Collectively, we propose SOX decoys as potential strategy for inhibiting SOX18 activity to disrupt tumour-induced neo-lymphangiogenesis.