On the structural basis and design guidelines for type II topoisomerase-targeting anticancer drugs

Abstract

Type II topoisomerases (Top2s) alter DNA topology via the formation of an enzyme–DNA adduct termed cleavage complex, which harbors a transient double-strand break in one DNA to allow the passage of another. Agents targeting human Top2s are clinically active anticancer drugs whose trapping of Top2-mediated DNA breakage effectively induces genome fragmentation and cell death. To understand the structural basis of this drug action, we previously determined the structure of human Top2 β-isoform forming a cleavage complex with the drug etoposide and DNA, and described the insertion of drug into DNA cleavage site and drug-induced decoupling of catalytic groups. By developing a post-crystallization drug replacement procedure that simplifies structural characterization of drug-stabilized cleavage complexes, we have extended the analysis toward other structurally distinct drugs, m-AMSA and mitoxantrone. Besides the expected drug intercalation, a switch in ribose puckering in the 3′-nucleotide of the cleavage site was robustly observed in the new structures, representing a new mechanism for trapping the Top2 cleavage complex. Analysis of drug-binding modes and the conformational landscapes of the drug-binding pockets provide rationalization of the drugs’ structural-activity relationships and explain why Top2 mutants exhibit differential effects toward each drug. Drug design guidelines were proposed to facilitate the development of isoform-specific Top2-targeting anticancer agents.

Interfacial inhibitors

“…5,26,27 In the case of Top2β, each monomer of the Top2 dimer accommodates one inhibitor molecules of the Top2-DNA cleavage complex (Top2cc) (Figure 3). 5 Similar mode of binding is observed in the case of the topoisomerase IV complex with the formation of a binding pocket at the protein-DNA interface when the binary system is subjected to treatment with a drug.…”

Structure-based design, synthesis and biological testing of etoposide analog epipodophyllotoxin–N-mustard hybrid compounds designed to covalently bind to topoisomerase II and DNA

“…The glycosidic moiety may even be replaced with a variety of other moieties such as the polyamines found in F14512 40 and in TOP-53 or a p -nitrophenyl moiety found in GL-311. 16 It has been shown in the PDB ID: 3QX3 X-ray structure of two molecules of etoposide complexed to cleaved DNA and topoisomerase IIβ 8,9 that the glycosidic moiety of etoposide occupies a spacious binding pocket in the protein with few protein interactions. This result explains why etoposide analogs are relatively insensitive to substituents that replace or substitute on the glycosidic moiety.…”

“…8,9 In this structure the glycosidic moiety of etoposide occupies a spacious binding pocket in the protein. The bound epipodophyllotoxin moiety of etoposide, unlike planar DNA intercalators that stack with two bases, stacks only with a single +5 guanine base in a DNA deformed structure.…”

“…The bound epipodophyllotoxin moiety of etoposide, unlike planar DNA intercalators that stack with two bases, stacks only with a single +5 guanine base in a DNA deformed structure. 9 Etoposide is an effective anticancer agent 10 and interfacial topoisomerase II inhibitor 11,12 which stabilizes a covalent topoisomerase II-DNA cleavable complex intermediate 10–14 resulting in single- and double-strand DNA breaks that are cytotoxic. Compounds in which the glycosidic moiety of etoposide is modified (e.g.…”

Pathways of cardiac toxicity: comparison between chemotherapeutic drugs doxorubicin and mitoxantrone

“…Wu et al (2013) determined the highresolution crystal structures of Top2β cleavage complexes stabilized by MTX. Huang and Lin (2014) demonstrated that this drug formed a weak cleavage complex with Top2β as compared with that formed with Top2α.…”