Cancer is one of the most widespread diseases and the second leading cause of death, with WHO reporting almost 10 million deaths annually. Human DNA topoisomerases comprise an important family of enzymes, molecular motors, that catalyze the induction of topological changes in the DNA molecule. Due to their ability to modulate the topology of the DNA molecule, these enzymes represent an important collection of targets for novel anticancer drugs. There are two forms of human DNA topoisomerase II: topoisomerase IIα in IIβ. The α isoform is preferentially expressed in proliferating cells, while the DNA β isoform is expressed at equal levels in quiescent and proliferating cells. Thus the DNA topoisomerase IIα represents a more attractive target for anticancer drug design.
Figure 1. Three-dimensional structure of the 43kDa dimmer of the ATPase domain of the human DNA topoisomerase IIα (PDB:1ZXM)
DNA Topoisomerase II targeting agents are classified into two major groups that differ in their mechanism of action. First, a more established group of molecules are named topoisomerase poisons, due to their role in stabilization of the short-lived covalent cleavage complex and conversion of this enzyme into a cellular toxin which is lethal to cancer cells. Current topoisomerase II inhibitors from this group in clinical practice (e.g Doxorubicin, Daunorubicin, Etoposide etc.), suffer from several side effects such as cardiotoxicity and induction of secondary malignancies. This is attributed to the induction of permanent double strand breaks (DBS) in the DNA molecule. Additionally emerging resistance to existing chemotherapeutics further fuels the need to develop new anticancer drugs.
To increase the safety profile of this proven chemotherapy approach and discover effective chemotherapeutic agents that inhibit the human DNA topoisomerase IIα , we take advantage of an alternative inhibition mechanism of its complex catalytic cycle and develop catalytic inhibitors that bind to its ATP pocket thus avoiding the DNA damage and lowering the chances of side effects associated with topo II poisons.
Our published reviews of DNA topoisomerase IIα molecular motor
- POGORELČNIK, Barbara, PERDIH, Andrej, ŠOLMAJER, Tomaž. Recent advances in the development of catalytic inhibitors of human DNA topoisomerase IIa as novel anticancer agents. Cur. Med. Chem., 2013, 20, 694-709. Link
- POGORELČNIK, Barbara, PERDIH, Andrej, ŠOLMAJER, Tomaž. Recent developments of DNA poisons - human DNA topoisomerase IIa inhibitors - as anticancer agents. Curr. Pharm. Design, 2013, 19, 2474-2488. Link
- BERGANT, Kaja, JANEŽIČ, Matej, PERDIH, Andrej. Bioassays and in silico methods in the identification of human DNA topoisomerase IIa inhibitors. Curr. Med Chem., 2018, 25, 3284-3316. Link
I. MOLECULAR SIMULATIONS OF TYPE II TOPOISOMERASES
We perform molecular simulations to derive a dynamic model of the N-terminal ATPase domain of topo IIα, where the ATP site is located, as well as study the flexibility of the entire topo II system during its catalytic cycle.
II. DESIGN OF CATALYTIC INHIBITORS OF TOPOISOMERASE II
With the help of available structural data on the structure of the ATPase domain of human DNA topoisomerase IIα, we are designing new catalytic inhibitors that would bind to the ATP binding site on the N-terminal ATPase domain of the enzyme and thus prevent the initiation of the catalytic cycle. We perform simulation-based optimization of lead compounds that would be suitable for further preclinical development to anticancer agents. The latter paradigm is not yet in use in cancer therapy.