Controlling Intramolecular Rotation with Five-Membered Heterocycles Facilitates the Design of Highly Cell-Permeable Xanthene-Based Fluorogenic Probes

Fluorogenic probes are invaluable tools in biology and medicine, offering high sensitivity and background-free imaging. However, achieving a high signal-to-noise ratio, target specificity, and robust cell permeability in wash-free imaging remains a significant challenge. Here, we report a new class of fluorogenic fluorophores engineered by incorporating five-membered heterocycles such as furan or thiophene at 9-position of the xanthene core. This structural modification enables precise control over intramolecular rotation, which is suppressed in viscous environments or upon interaction with biomolecular targets to allow for fluorescence activation independent of the spirolactone equilibrium characteristic of traditional rhodamine fluorophores. This rotation-based activation strategy was further extended to develop furan- and thiophene-substituted carborhodamine and silicon-rhodamine fluorophores, demonstrating the versatility and modularity of our approach. Using this design, we developed practical fluorogenic probes for self-labeling protein tags, including HaloTag, SNAP-tag, and PYP-tag, achieving high cell permeability and strong fluorescence activation under no-wash live-cell imaging conditions. The HaloTag probe enabled real-time visualization of the endoplasmic reticulum whorl formation in live cells, showcasing its utility in dynamic cellular imaging. To enhance the applicability of our design, we developed BRD4- and EGFR-targeting probes by conjugating our fluorophores with JQ1 and gefitinib/erlotinib inhibitors, utilizing a non-covalent binding strategy. The EGFR-targeting probes exhibited strong fluorescence in cells with high levels of EGFR expression, demonstrating their effectiveness for detecting EGFR overexpression. This work presents a versatile design strategy that leverages the controlled intramolecular rotation of furan/thiophene rings to create innovative OFF/ON fluorogenic probes, offering a robust platform for selective, wash-free live-cell imaging of diverse cellular targets.