Lighting up POLRMT: Computational discovery of a selective and " Off–On " fluorescent probe for cancer theranostics

Abstract

Human mitochondrial RNA polymerase (POLRMT), a critical enzyme for mitochondrial DNA transcription, is frequently overexpressed in various tumors, including colorectal cancer, where it drives cancer progression. Specific targeting of POLRMT not only holds promise for suppressing cancer cell growth but also provides a novel molecular tool for cancer diagnosis through direct visualization. However, imaging strategies for POLRMT are currently underdeveloped, which restricts its translational potential. To address this gap, we present the rational design and characterization of a novel fluorescent probe based on the Folding-Photoinduced Electron Transfer (PET) mechanism. Our approach integrated structure-driven drug design with molecular dynamics simulations. The resulting probe, BMXan–ImPy, was constructed by combining the pharmacophore recognition unit BMXan with the optical module ImPy, and its fluorescence mechanism was validated through quantum chemical calculations. In the free state, BMXan–ImPy adopts a folded conformation that facilitates PET, leading to quenched fluorescence. Upon binding to POLRMT, the interaction induces conformational unfolding, which blocks the PET process and restores fluorescence, enabling highly specific “Off–On” imaging. Experimental studies in colorectal cancer cells demonstrated that BMXan–ImPy exhibits strong biological activity and favorable optical properties. This work introduces the first POLRMT-targeted theranostic small-molecule probe, underscoring its potential as a promising strategy and technical platform for the early diagnosis and precision therapy of colorectal cancer.