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Design of novel anticancer Agents

1. Road to safer chemoterapeutics: Design of catalytic inhibitors of human DNA topoisomerase IIα

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.

    Figure 2. Ouline of the design paradigm of catalytic inhibitors of human topoisomerase IIα that would bind to its ATP binding site at the N-terminal/ATPase domain of the enzyme and thus prevent initiation of the catalytic cycle.

    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 agentsCur. Med. Chem.201320, 694-709. Link
    • POGORELČNIK, Barbara, PERDIH, Andrej, ŠOLMAJER, Tomaž. Recent developments of DNA poisons - human DNA topoisomerase IIa inhibitors - as anticancer agents. Curr. Pharm. Design201319, 2474-2488. Link
    • BERGANT, Kaja, JANEŽIČ, Matej, PERDIH, Andrej. Bioassays and in silico methods in the identification of human DNA topoisomerase IIa inhibitorsCurr. Med Chem.201825, 3284-3316. Link

    In our research, we take advantage of the drug discovery cycle paradigm. The starting point for our design efforts is the available structural information about the conformation of the ATPase domain. We use computational design methods such as molecular docking calculations and various pharmacophore modeling approaches. We complement these data with molecular simulations. The compounds we design are first tested in various biochemical assays and then characterized in biophysical experiments (e.g. surface plasmon resonance (SPR) and microscale thermophoresis (MST)) using only the ATPase domain. In collaboration with experimental partners, we are also determining the citotoxicity of the compounds on various cancer cell lines to evaluate the preclinical anticancer potential of these compounds. The data we obtain feed the next itation of the described experiments.

    Figure 3. Schematic representation of our design process for new human topoisomrase IIα catalytic inhibitors identification.


    Our development of catalytic inhibitors of human DNA topoisomerase IIα


    BERGANT LOBODA, Kaja, JANEŽIČ, Matej, ŠTAMPAR, Martina, ŽEGURA, Bojana, FILIPIČ, Metka, PERDIH, Andrej. Substituted 4,5'-bithiazoles as catalytic inhibitors of human DNA topoisomerase IIαJournal of chemical information and modeling. 2020, 60, 3662-3678. Link,  EP Patent Application     

    JANEŽIČ, Matej, VALJAVEC, Katja, BERGANT LOBODA, Kaja, HERLAH, Barbara, OGRIS, Iza, KOZOROG, Mirijam, PODOBNIK, Marjetka, GOLIČ GRDADOLNIK, Simona, WOLBER, Gerhard, PERDIH, Andrej. Dynophore-based approach in virtual screening : a case of human DNA topoisomerase IIα. International journal of molecular sciences 2021, 22(24), 13474 Full text

    BERGANT LOBODA, Kaja, VALJAVEC, Katja, ŠTAMPAR, Martina, WOLBER, Gerhard, ŽEGURA, Bojana, FILIPIČ, Metka, SOLLNER DOLENC, Marija, PERDIH, Andrej. Design and synthesis of 3,5-substituted 1,2,4-oxadiazoles as catalytic inhibitors of human DNA topoisomerase IIα. Bioorganic chemistry2020, 99, 103828. Link

    BERGANT  Kaja, JANEŽIČ Matej, VALJAVEC Katja, SOSIČ Izidor, PAJK Stane, ŠTAMBAR Martina, ŽEGURA Bojana, GOBEC Stanislav, FILIPIČ Metka, PERDIH Aandrej. Structure-guided optimization of 4,6-substituted-1,3,5-triazin-2(1H)-ones as catalytic inhibitors of human DNA topoisomerase IIαEuropean Journal of Medicinal Chemistry2019, 175, 330-348. Link

    POGORELČNIK, Barbara, BRVAR, Matjaž, ŽEGURA, Bojana, FILIPIČ, Metka, ŠOLMAJER, Tomaž, PERDIH, Andrej. Discovery of mono and bi-substituted 1H-Pyrazolo[3,4]Pyrimidines and 9H-Purines As Catalytic Inhibitors of Human DNA Topoisomerase IIα. ChemMedChem2015, 10, 345-359. Link

    POGORELČNIK, Barbara, JANEŽIČ, Matej, SOSIČ, Izidor, GOBEC, Stanislav, ŠOLMAJER, Tomaž, PERDIH, Andrej. 4,6- substituted-1,3, 5-triazin-2(1H)-ones as monocyclic catalytic inhibitors of human DNA topoisomerase IIα targeting the ATP binding siteBioorganic & Medicinal Chemistry2015, 234218-4229. Link


    POGORELČNIK, Barbara, BRVAR, Matjaž, ZAJC, Irena, FILIPIČ, Metka, ŠOLMAJER, Tomaž, PERDIH, Andrej. Monocyclic 4-amino-6-(phenylamino)-1,3, 5-triazines as inhibitors of human DNA topoisomerase IIαBioorganic & Medicinal Chemistry Letters2014, 24, 5762-5768. Link



    JANEŽIČ, Matej, POGORELČNIK, Barbara, BRVAR, Matjaž, ŠOLMAJER, Tomaž, PERDIH, Andrej. 3-substituted-1H-indazoles as catalytic inhibitors of the human DNA topoisomerase IIα. ChemistrySelect2017, 2, 480-488. Link

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