Identification of novel human topoisomerase III beta inhibitors

Human topoisomerase III beta (TOP3B) is a type IA topoisomerase that can change the topology of DNA and RNA substrates via a phosphotyrosine covalent intermediate. TOP3B has been shown to be required for the efficient replication of certain positive-sense ssRNA viruses including Dengue. We applied molecular dynamics simulation combined with docking studies to identify potential inhibitors of TOP3B from a library comprised of drugs that are FDA-approved or undergoing clinical trials for potential drug repurposing. Topoisomerase activity assay of the top virtual screening hits showed that bemcentinib, a compound known to target the AXL receptor tyrosine kinase, can inhibit TOP3B relaxation activity. Additional small molecules that share the N5,N3-1H-1,2,4-triazole-3,5-diamine moiety of bemcentinib were synthesized and tested for inhibition of TOP3B relaxation activity. Five of these molecules showed comparable IC₅₀ as bemcentinib for inhibition of TOP3B. However, these five molecules had less selectivity towards TOP3B inhibition versus bemcentinib when inhibition of the type IB human topoisomerase I was com-pared. These results suggest that exploration of tyrosine kinase inhibitors and their analogs may allow the identification of novel topoisomerase inhibitors.