Identification and characterization of topoisomerase III beta poisons

Significance

Topoisomerase poisons that trap topoisomerase I and II (TOP1 and TOP2) have long been important agents in anticancer therapy and for elucidating the cellular functions of TOP1 and TOP2. However, poisons for topoisomerase III have never been reported. Topoisomerase III beta (TOP3B) is the only topoisomerase with a dual activity on RNA as well as DNA and has recently been reported to ensure genome stability, chromatin accessibility, R-loops resolution, and potentially the replication of positive-sense RNA viruses, including dengue and SARS-CoV-2. In our study, we designed and carried out a chemical screen for poisons that trap human TOP3B. Among the most active inhibitors, we report and characterize in vitro and cellular trapping of TOP3B by bisacridine and thiacyanine compounds.

Abstract

We designed and carried out a high-throughput screen for compounds that trap topoisomerase III beta (TOP3B poisons) by developing a Comparative Cellular Cytotoxicity Screen. We found a bisacridine compound NSC690634 and a thiacyanine compound NSC96932 that preferentially sensitize cell lines expressing TOP3B, indicating that they target TOP3B. These compounds trap TOP3B cleavage complex (TOP3Bcc) in cells and in vitro and predominately act on RNA, leading to high levels of RNA-TOP3Bccs. NSC690634 also leads to enhanced R-loops in a TOP3B-dependent manner. Preliminary structural activity studies show that the lengths of linkers between the two aromatic moieties in each compound are critical; altering the linker length completely abolishes the trapping of TOP3Bccs. Both of our lead compounds share a similar structural motif, which can serve as a base for further modification. They may also serve in anticancer, antiviral, and/or basic research applications.