Nature-inspired substituted 3-(imidazol-2-yl) morpholines targeting human topoisomerase IIα: Dynophore-derived discovery

• Published in: Biomedicine & pharmacotherapy 2024-06, Vol.175, p.116676, Article 116676
• Main Authors: Herlah, Barbara, Janežič, Matej, Ogris, Iza, Grdadolnik, Simona Golič, Kološa, Katja, Žabkar, Sonja, Žegura, Bojana, Perdih, Andrej
• Format: Article
• Language: English
• Subjects: Cancer; Catalytic inhibitors; Chemotherapy; DNA damage; Topoisomerase II
• ISSN: 0753-3322; 1950-6007; 1950-6007
• DOI: 10.1016/j.biopha.2024.116676

The molecular nanomachine, human DNA topoisomerase IIα, plays a crucial role in replication, transcription, and recombination by catalyzing topological changes in the DNA, rendering it an optimal target for cancer chemotherapy. Current clinical topoisomerase II poisons often cause secondary tumors as side effects due to the accumulation of double-strand breaks in the DNA, spurring the development of catalytic inhibitors. Here, we used a dynamic pharmacophore approach to develop catalytic inhibitors targeting the ATP binding site of human DNA topoisomerase IIα. Our screening of a library of nature-inspired compounds led to the discovery of a class of 3-(imidazol-2-yl) morpholines as potent catalytic inhibitors that bind to the ATPase domain. Further experimental and computational studies identified hit compound 17, which exhibited selectivity against the human DNA topoisomerase IIα versus human protein kinases, cytotoxicity against several human cancer cells, and did not induce DNA double-strand breaks, making it distinct from clinical topoisomerase II poisons. This study integrates an innovative natural product-inspired chemistry and successful implementation of a molecular design strategy that incorporates a dynamic component of ligand-target molecular recognition, with comprehensive experimental characterization leading to hit compounds with potential impact on the development of more efficient chemotherapies. [Display omitted] •Development of topo IIα inhibitors with dynophore-derived molecular design.•Discovery of nature-inspired 3-(imidazol-2-yl) morpholines as hit compounds.•Catalytic inhibition mechanism and confirmed binding to the isolated ATPase domain.•Selective inhibition of topo IIα over a range of human protein kinases.•Identification of sensitive cell lines and observation of decreased DNA damage.