Two-in-one combination therapy of fluoronucleoside analogues and triplex forming oligonucleotides

Antigene technology based on triplex-forming oligonucleotide (TFO) has been widely used in gene-specific regulation, serving as a potential gene therapy method. The optimization of TFO backbone and base can significantly improve the formation and stability of the triplex DNA. Fluorination is widely used in small molecule drug development, but its application in TFO optimization has not been well characterized. Herein, we developed a ‘in silico-in vitro-in vivo’ screening strategy to optimize fluorine atom (F) substitution of TFO. Molecular dynamics simulations are applied to screen single-site F substitutions in the TFO bases that retained stable triplex formation ability with the Ets2-targeted duplex DNA. Combining existing nucleotide analogue floxuridine, the synergistic effect is realized via a two-in-one chemo-TFO including gene regulation and chemotherapeutic functions, which is verified through in vitro and in vivo anti-tumor experiments.