Covalent Complex Model of DNA Topoisomerase and DNA for Molecular Dynamics Simulation

Abstract

DNA topoisomerase is responsible for regulation of DNA topological state. The relaxation of supercoiled DNA is catalyzed by DNA topoisomerase. Upon interaction, DNA topoisomerase form a transient covalent linkage with DNA. This transient covalent complex can be trapped using topoisomerase inhibitors and these inhibitors have a potential to be developed as a new class of drugs targeting topoisomerase. In Escherichia coli (E. coli), accumulation of topoisomerase I (topoI)-DNA complex leads to bacterial cell death. We have designed a model of the complex to be investigated using molecular dynamics (MD) simulations. This model allowed us to study topoisomerase-DNA covalent system using computer simulations incorporating structural flexibility as well as effect of small molecule in the topoisomerase-DNA interaction. As an example, we used E. coli topoisomerase I (EctopoI), which is the most extensively studied bacterial type IA topoI and a target for antibacterial drug discovery. Utilizing our model, we first simulated the EctopoI-DNA covalent complex and then performed screening of a library of compounds against the minimized EctopoI target, using virtual screening, to identify potential EctopoI inhibitors. Finally, taking one of the identified inhibitors, we investigated the dynamics of ternary complex of EctopoI, inhibitor, and DNA. Our simulation results show that both the EctopoI-DNA binary complex as well as EctopoI-inhibitor-DNA ternary complex were stable for 50 ns of MD simulations. Our results further imply that the identified inhibitor prevents relegation of the cleaved DNA, which leads to accumulation of the EctopoI-inhibitor-DNA ternary complex.