Drug-induced conformational population shifts in topoisomerase-DNA ternary complexes.

Nan-Lan Huang,Jung-Hsin Lin

doi:10.3390/molecules19067415

Abstract

Type II topoisomerases (TOP2) are enzymes that resolve the topological problems during DNA replication and transcription by transiently cleaving both strands and forming a cleavage complex with the DNA. Several prominent anti-cancer agents inhibit TOP2 by stabilizing the cleavage complex and engendering permanent DNA breakage. To discriminate drug binding modes in TOP2-α and TOP2-β, we applied our newly developed scoring function, dubbed AutoDock4RAP, to evaluate the binding modes of VP-16, m-AMSA, and mitoxantrone to the cleavage complexes. Docking reproduced crystallographic binding mode of VP-16 in a ternary complex of TOP2-β with root-mean-square deviation of 0.65 Å. Molecular dynamics simulation of the complex confirmed the crystallographic binding mode of VP-16 and the conformation of the residue R503. Drug-related conformational changes in R503 have been observed in ternary complexes with m-AMSA and mitoxantrone. However, the R503 rotamers in these two simulations deviate from their crystallographic conformations, indicating a relaxation dynamics from the conformations determined with the drug replacement procedure. The binding mode of VP-16 in the cleavage complex of TOP2-α was determined by the conjoint use of docking and molecular dynamics simulations, which fell within a similar binding pocket of TOP2-β cleavage complex. Our findings may facilitate more efficient design efforts targeting TOP2-α specific drugs.

Highlights

Topoisomerase is a prominent family of enzymes that manipulate DNA topology to release the supercoiling force introduced after DNA replication or transcription [1]
VP-16 and other currently used TOP2-targeting anticancer drugs are suggested to be the “poisons” of both TOP2-α and TOP2-β [8,9,10], which increase the formation of covalent cleavage complex and hamper re-ligation of the cleaved DNA
Because it is the first ternary complex crystalized after the drug was stabilized in the cleavage complex, we started with this structure for molecular docking with the use of AutoDock4RAP

Summary

Introduction

Topoisomerase is a prominent family of enzymes that manipulate DNA topology to release the supercoiling force introduced after DNA replication or transcription [1]. Eukaryotic type II topoisomerases (Top2) are multimeric enzymes that engender double-strand breaks of DNA. VP-16 and other currently used TOP2-targeting anticancer drugs are suggested to be the “poisons” of both TOP2-α and TOP2-β [8,9,10], which increase the formation of covalent cleavage complex and hamper re-ligation of the cleaved DNA. The growing knowledge on these structures can be promising in the design of new compounds that target the cleavage complex of TOP2-α. We have validated AutoDock4RAP on evaluating the binding affinities of glycans to lectins [25] The use of this robust scoring function may facilitate virtual screening on compounds with more diverse chemical scaffolds. We employed AutoDock4RAP to evaluate the binding affinities of VP-16, m-AMSA, and mitoxantrone to the TOP2-DNA complexes. The term “cleavage complex” will be used to describe the enzyme-DNA complex, and the cleavage complex bound with small molecule drugs will be referred to as a “ternary complex”

Results and Discussion

Protein Models of TOP2-α and TOP2-β

Molecular Docking with the Use of AutoDock4RAP

Interaction Diagrams

Conclusions