Drugging topoisomerases: lessons and challenges

Abstract

Topoisomerases are ubiquitous enzymes that control DNA supercoiling and entanglements. They are essential during transcription and replication, and topoisomerase inhibitors are among the most effective and most commonly used anticancer and antibacterial drugs. This review consists of two parts. In the first part ("Lessons"), it gives background information on the catalytic mechanisms of the different enzyme families (6 different genes in humans and 4 in most bacteria), describes the "interfacial inhibition" by which topoisomerase-targeted drugs act as topoisomerase poisons, and describes clinically relevant topoisomerase inhibitors. It generalizes the interfacial inhibition principle, which was discovered from the mechanism of action of topoisomerase inhibitors, and discusses how topoisomerase inhibitors kill cells by trapping topoisomerases on DNA rather than by classical enzymatic inhibition. Trapping protein-DNA complexes extends to a novel mechanism of action of PARP inhibitors and could be applied to the targeting of transcription factors. The second part of the review focuses on the challenges for discovery and precise use of topoisomerase inhibitors, including targeting topoisomerase inhibitors using chemical coupling and encapsulation for selective tumor delivery, use of pharmacodynamic biomarkers to follow drug activity, complexity of the response determinants for anticancer activity and patient selection, prospects of rational combinations with DNA repair inhibitors targeting tyrosyl-DNA-phosphodiesterases 1 and 2 (TDP1 and TDP2) and PARP, and the unmet need to develop inhibitors for type IA enzymes.

Figure 1

Differential catalytic mechanisms of topoisomerases. Reactions are represented from left to right. Type I enzymes cleave one strand to process DNA entanglements whereas type II cleave both strands by concerted action of each Top2 monomer (see Table 1). Type IA and IIA enzymes (panels A and C) cleave DNA by covalently attaching their catalytic tyrosine to the DNA 5’-end. Type IA enzymes cleave a single-stranded segment and let another single-strand pass through the break, whereas type IIA let a duplex pass through the concerted breakage of both strands. For both type IA and IIA enzymes, the 3’-ends are tightly bound during strand passage, which keeps the passing DNA in an enzyme cavity before resealing of the ends (not shown; for details see ^,,). By contrast to type IA and IIA enzymes, type IB topoisomerases (panel B) form 3’-phosphotyrosine bonds and relax DNA supercoiling by controlled rotation of the broken 5’-end around the intact strand.^,

Figure 2

Interfacial inhibition for Top1 (left) and Top2 inhibitors (right). Under normal conditions, Top1 and Top2 cleave and religate DNA very rapidly (A–B and E–F). Religation is faster than cleavage and cleavage complexes are transient. Drugs (green) (C–D and G–H) bind reversibly (C and G) at the interface of the cleaved DNA and the enzyme by forming a ternary complex (see text for details). The pdb coordinates for D and H are 1T8I and 3QX3, respectively.

Figure 3

Structure of anticancer and antibacterial topoisomerase inhibitors. A: Camptothecins. B: Non-camptothecin Top1 inhibitors in clinical trials. C: Anthracyclines. D: Demethylepipodophyllotoxin derivatives, including the clinical trial drug F14512 with its spermine side chain. E: Other Top2cc-targeted intercalative drugs. F: Three Top2cc-targeted drugs in clinical trials in addition to F14512 shown in panel D. G: Top2 catalytic inhibitors. G: Quinolone antibacterials.

Figure 4

Schematic representation of the two main repair pathways removing topoisomerase-DNA complexes.