Synthesis and photodynamic activity of novel thieno[3,2–b]thiophene fused BODIPYs with good bio-solubility and anti-aggregation effect

•A series of novel thieno[3,2–b]thiophene-fused BODIPY derivatives with water-soluble groups were designed, synthesized and evaluated.•These compounds exhibited NIR absorptions (∼660 nm) and high molar extinction coefficients (0.73 × 105-1.42 × 105 M−1·cm−1).•These compounds possessed good singlet oxygen generation and photodynamic anti Eca-109 cancer cells abilities.•Compound II4 could be well uptaked by Eca-109 cells, and showed much better photodynamic efficiency both in vitro and in vivo than Temoporfin.