Smoothed Potential Md Simulations For Dissociation Kinetics Of Etoposide To Unravel Isoform Specificity In Targeting Human Topoisomerase Ii

Human type II topoisomerases (Topoll) are essential for controlling DNA topology within the cell. For this reason, there are a number of Topoll-targeted anticancer drugs that act by inducing DNA cleavage mediated by both TopoII isoforms (TopoII alpha and TopoII beta) in cells. However, recent studies suggest that specific poisoning of TopoIIa may be a safer strategy for treating cancer. This is because poisoning of TopoII beta appears to be linked to the generation of secondary leukemia in patients. We recently reported that enzyme-mediated DNA cleavage complexes (in which TopoII is covalently linked to the cleaved DNA during catalysis) formed in the presence of the anticancer drug etoposide persisted approximately 3-fold longer with TopoII alpha than TopoII beta. Notably, enhanced drug-target residence time may reduce the adverse effects of specific Topolla poisons. However, it is still not clear how to design drugs that are specific for the alpha isoform. In this study, we report the results of classical molecular dynamics (MD) simulations to comparatively analyze the molecular interactions formed within the TopoII/DNA/etoposide complex with 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 residues (Ser763 and Ser800) in TopoIIa. These interactions are missing in TopoII beta, where both amino acids are alanine residues. This may explain the greater persistence of etoposide-stabilized cleavage complexes formed with Topo TopoIIa. These findings could be useful for the rational design of specific Topolla poisons.