The cancer burden in the European Union is huge. Cancer is the second most common cause of death in the E.U., with more than 3.9 million new cases and 1.9 million deaths each year.¹ Sharing 9% of the world population, Europe shares 25% of the global cancer burden. Unfortunately, the current anticancer drugs often induce harmful side effects (such as treatment-related acute myeloid leukemia (AML)) that diminish their efficacy. Additionally, the frequent development of drug resistance hampers the drug action against cancer and bacterial infections, further enhancing the socio-economic burden.

^{1. Ferlay et al. Eur. J. Cancer, 2018, 103, 356.}

1. Dynamic Docking Studies of Human TopoII Bound to Potential TopoII Inhibitors. Etoposide targets both TopoIIα and TopoIIβ. However, how the two enzyme isoforms affect the therapeutic/inhibitor properties of the drug is unclear. To develop an etoposide-based drug with specificity for cancer cells the sugar moiety of the drug has been previously replaced with a polyamine tail. Such inhibitors would be preferentially taken up by cancer cells, which have an active polyamine transport system, thereby lessening off-target effects in noncancerous cells. To understand the effects of this substitution on the specificity of hybrid molecules toward the two enzyme isoforms, we analyzed the activity of a series of etoposide-polyamine hybrids toward human topoisomerase IIα and IIβ. All of these compounds induce higher/comparable enzyme-mediated DNA cleavage than induced by etoposide. Relative to the parent drug, the hybrid compounds displayed substantially higher activity toward topoisomerase IIβ than IIα. In collaboration with Prof. Neil Osheroff, Vanderbilt University, we provided the basis for the enhanced specificity of polyamine derivatives of etoposide to TopoIIβ. ^{(Bioorg. Med. Chem. Lett. 28 (2018) 2961.)} Our enzymology and modeling studies have generated a testable hypothesis for the design of future drugs with enhanced specificity toward a single isoform of human topoisomerase II. Link

2. Classical and Smoothed Potential MD Simulations to Unravel Isoform Specificity in Targeting Human TopoII Current clinical TopoII poisons are nonspecific with regard to TopoIIα and TopoIIβ and affect the DNA cleavage activity of both isoforms. However, strong support has been provided by both cellular and in vivo studies that TopoIIβ is primarily responsible for generating the breaks in the mixed lineage leukemia (MLL) gene that initiates the acute myelogenous leukemias associated with etoposide treatment. These studies suggest that TopoIIα-specific poisoning might help mitigate the side effects observed with nonspecific TopoII drugs. However, the rational design of TopoIIα selective inhibitors is difficult as the two isoforms share approximately 78% identity at the catalytic site, differing only in two amino acids. In our previous work, ^{(Bioorg. Med. Chem. Lett. 28 (2018) 2961)} we reported that enzyme-mediated DNA cleavage complexes, with TopoII covalently linked to the cleaved DNA during catalysis, formed in the presence of the anticancer drug etoposide persisted approximately 3-fold longer with TopoIIα than TopoIIβ. Notably, the enhanced drug-target residence time may reduce the adverse effects of specific TopoIIα poisons. To clarify how to design drugs that are specific for the α isoform, we employed classical molecular dynamics (MD) simulations to comparatively analyze the molecular interactions formed within the TopoII/DNA/etoposide complex in both isoforms. We also used smoothed potential MD to estimate etoposide dissociation kinetics from the two isoform complexes. These extensive classical and enhanced sampling simulations revealed stabilizing interactions of etoposide with two serine amino acid residues in TopoIIα. These interactions are missing in TopoIIβ, where both amino acids are alanine residues. This may explain the greater persistence of etoposide-stabilized cleavage complexes formed with TopoIIα. The findings of our study provide a structural and kinetic rationale for the design of novel TopoIIα-specific drugs, which can stably engage these serine residues. Link

3. Dynamic Docking to Elucidate the Interactions of TopoII and a New Class of TopoII Inhibitors. Based on previously reported hybrid TopoII inhibitors that merge key pharmacophoric elements of etoposide and merbarone, work was done to further expand this molecular entity by synthesizing sixteen additional hybrid derivatives. Working with organic chemists and biochemists, dynamic docking studies were performed to identify the important interactions stabilizing the new hybrid TopoII inhibitors in complex with the target. Most of these new compounds exhibited good inhibitory activity and cytotoxicity in three cancer cell lines with an IC50 in the low micromolar range. Hence, understanding the key molecular features needed for the drug-like properties in this novel chemical series of TopoII targeting compounds will aid in developing the new structural motif as a potential TopoII poison.

To see the dissociation of etoposide (anti-cancer drug) from human TopoII, click here