Topoisomerase is a class of enzymes that alter the supercoiling of double-stranded DNA. (In supercoiling the DNA molecule coils up like a telephone cord, which shortens the molecule.) The topoisomerases act by transiently cutting one or both strands of the DNA. Topoisomerase type I cuts one strand whereas topoisomerase type II cuts both strands of the DNA to relax the coil and extend the DNA molecule.

Topoisomerases, often called the magicians of DNA world, are ubiquitous proteins found in all domains of life. Relieving the torsional stress in the DNA double helix generated during replication, transcription, recombination and repair, topoisomerases solve all of the topological problems of DNA. The torsional stress during the nuclear process is relieved by allowing the DNA strands or double helices to pass through each other. This is achieved by topoisomerases introducing nicks in the DNA strands. Considering the activity of topoisomerases in the process of DNA replication, in recent years DNA topoisomerases have emerged as chief targets for several potent anti-cancer agents.

There are six types of topoisomerases, but most researchers focus on two because of their significance in cell proliferation, topoisomerase type I and topoisomerase type II. Type I has two subtypes, type IA and type IB. They alter DNA by creating a single strand break or “cut” into a single DNA strand followed by the other opposite strand passing through the break and/or by a controlled mechanism of the topological region of the strand around where the break occurs, which is where type IIB comes in. Type IA topoisomerases, in general, need divalent metal ions, (most commonly Mg2+), for DNA scission and attach covalently to the phosphate group found on the 50-teriminal end of DNA. Type IB enzymes are the opposite in needing a metal for catalysis, they also covalently link to a phosphate group, but this group is located on the 30 terminal of DNA. Due to these facts, Type I topoisomerases, can under and over wind DNA, but not unwind or detangle DNA, in particular catenae like DNA or supercoiled.

Type II topoisomerases need divalent metal ions (most commonly Mg2+) and ATP to complete catalytic performances. These enzymes create double stranded breaks that were determined in different steps. The steps are as follows: the enzyme binds to two separate segments of DNA, creates a double stranded break in one segment, translocates the second DNA segment through the cleaved nucleic acid ‘gate’, rejoin or ligate the cleaved DNA, releases the translocated segment through a gate in the protein and close the protein gate, and manifests itself to start a new circulation of catalysis performances. These enzymes are the better choice for DNA replication progression due to their double-stranded passage mechanism. Once this mechanism occurs, this type can unknot and untangle supercoiled DNA, unlike its counter, type I. Thus, within the thesis, type II will be of interest.

Topoisomerase enzyme inhibitors are a class of drugs acting directly on the cells. A diverse set of anti-cancer agents like camptothecin, camptothecin derivatives and noncamptothecins target DNA topoisomerase I by acting as topoisomerase I enzyme inhibitors. Topoisomerase I inhibitors bind to the topoisomerase I-DNA cleavage complex, preventing the religation and inhibiting the resealing of single strand nicks.The catalytic mechanism of topoisomerases leading to strand breakage involves attack of DNA phosphorus by tyrosyl oxygen of the enzyme thus forming a covalent phosphotyrosine link. This results in the breakage of the DNA phosphodiester bond at the same time. The second trans-esterification, which is the reverse of the first, results in the rejoining of the DNA strands. This involves attack of oxygen of DNA hydroxyl group generated in the first reaction on phosphorus of the phosphotyrosine link. This results in the breakage of the covalent bond formed between the enzyme and DNA.

Reference: Alexis Sledge. The Synthesis of Novel Fluorinated 9-Amino Acridones as Potential Topoisomerase IIα Poisons

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