DNA topoisomerase IIα (topo IIα) is a key enzyme in the regulation of DNA topology and plays a central role in replication, transcription and cell division. Due to its increased expression in rapidly dividing cancer cells, it represents an important target for anticancer drugs. Most clinically used topo IIα inhibitors act as topoisomerase poisons, stabilizing the DNA–enzyme complex and causing the accumulation of DNA double-strand breaks, which is associated with severe side effects and the risk of secondary cancers. Catalytic inhibitors that inhibit the enzyme without inducing DNA damage are therefore a promising alternative.
The focus of this master thesis was the computer-aided optimization, synthesis and biological evaluation of 4,6-disubstituted 1,3,5-triazin-2(1H)-ones as catalytic inhibitors of human DNA topo IIα, targeting the ATP binding site. To expand our knowledge of the structure-activity relationship (SAR) of triazinones with bridging oxygen atoms (O-triazinones), we prepared a small series of new analogues with a bicyclic substituent or new monocyclic substituents at position 6 using the developed synthesis procedure.
Biological evaluation of the synthesized O-triazinones showed that compound 8 had the strongest inhibitory activity, with better potency than the clinically used topoisomerase poison etoposide. We also demonstrated that the introduction of bicyclic substituents at position 6 of the triazinone ring, similar to S-triazinones, allows inhibition of topo IIα with comparable activity. The compound acts as a catalytic inhibitor and does not stabilize the covalent DNA–enzyme complex. The results of molecular docking showed the preservation of the interaction pattern with the ATP binding site as determined for a previous series of O-triazinones. Using the DeepFrag design program, which is based on deep learning and molecular docking methods, we then also designed new substituents at positions 4 and 6 of the triazinone scaffold Among the evaluated in silico compounds, the potential introduction of a sulfonic or sulfonamide group on the phenyl ring attached at the substitution site 4, as a possible mimetic of one of the phosphate groups of the ATP molecule, proved to be particularly interesting. The master's thesis contributes to the further development of the class of triazinone catalytic topo IIα inhibitors and confirms the utility of deep learning methods in structure-based optimization of biologically active compounds in the early stages of anticancer drug discovery.
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