Deciphering protein-DNA interactions of with transcription factors through molecular docking, molecular dynamics simulations, and gene expression analysis.

Metastasis is a key hallmark of cancer aggressiveness, particularly in triple-negative breast cancer (TNBC), which lacks effective targeted therapies. Kisspeptin-1 (KISS1), a known metastasis suppressor is emerging as a potential therapeutic modulator. This study investigates the structural and regulatory interactions between and key transcription factors (TFs) involved in metastasis: SP1, CDX2, FLI1, GATA2, NMYC, and HDAC2. TFs were identified TFLink, modelled using SWISS-MODEL, and docked with -DNA using HADDOCK. CDX2 showed the strongest binding (HADDOCK score: -144.2; buried surface area: 2526.5 Å), followed by HDAC2, GATA2, NMYC, SP1, and FLI1. Molecular dynamics simulations (150 ns) revealed stable complexes for SP1, NMYC, and CDX2 with low RMSD (2.1-2.7 Å), compact Rg (∼21.0 Å), and stable hydrogen bonding (5-9 bonds). In contrast, FLI1 and GATA2 showed greater flexibility and unstable interactions. Experimental validation in MDA-MB-231 cells treated with Kisspeptin-10 (IC: 100.21 nM) showed upregulation of SP1, NMYC, CDX2, and GATA2, and downregulation of FLI1 and HDAC2. These findings suggest KISS1 selectively modulates transcriptional activity toward anti-metastatic signaling. Overall, demonstrates strong potential as a transcriptional regulator and therapeutic agent against TNBC metastasis.