Single-molecule FRET-based approach for protein-targeted drug discovery

Many therapeutic drugs target various proteins involved in diverse biological processes. Among these proteins, type II topoisomerases are critical targets for anticancer and antibacterial chemotherapies, yet the action mechanisms of many type II topoisomerase-targeting drugs have not been fully elucidated. In this regard, the development of rapid and accurate methods to identify the mode of action of potential drug candidates is crucial to improve the efficiency of drug screening and discovery. Here, using type II topoisomerase as a model system, we present a single-molecule fluorescence resonance energy transfer-based drug screening method capable of delineating when and how the drug candidates participate in the entire reaction steps of the target protein. This unique capability has been demonstrated to be applicable to the identification of representative types of widely prescribed drugs targeting type II topoisomerase: etoposide which stabilizes the enzyme-DNA cleavage complex, and bisdioxopiperazines (ICRF-I93) which lock the N-terminal gate of the enzyme into the closed state. Based on this demonstration experiment, we expect that our proposed method will be extended to broad applications in the screening of potent drugs targeting various proteins.