Topoisomerases cleavage reaction

The interaction of ellipticine derivatives with topoisomerase II enzymes in Plasmodium berghei (163), a parasite of mouse red blood cells, mouse lymphoma L5178Y cells (164), simian virus 40 CV-1 cells (165), Trypanosoma cruzi (166,167), and the human small-cell lung cancer cell line NCI N417 (168,169) has been studied. In the latter study, the highest in vitro activity in the topoisomerase II-DNA cleavage reaction and decatenation was observed for elliptinium (5) and datelliptium (384) (769). 

It is clear that some DNA transformations can be accomplished by the cleavage of a single DNA strand while others (such as catenation of two closed-circular duplexes) must involve cleavage of both strands. This has led to the classification of topoisomerases whose reactions proceed via a transient single-strand break as type I, while enzymes whose reactions proceed via double-strand breaks are described as type II (Liu et al.,... 

Figure 28.50 Recombinases and topoisomerase i. A superposition of Cre recombinase (blue) and topoisomerase I (orange) reveals that these two enzymes have a common structural core. The positions of the tyrosine residues that participate in DNA cleavage reactions are shown as red spheres for both enzymes. [Drawn from 2CRX.pdb and 1A31.pdb.]...

Type I and type II topoisomerases relax negatively supercoiled DNA in steps of one and steps of two, respectively. Type II topoisomerases can also add additional negative supercoils (as indicated by the double arrow). The latter reaction requires energy input, which is encoded by ATP cleavage. 

Straub T, Boesenberg C, Gekeler V, Boege F (1997) The dihydropyridine dexniguldipine hydrochloride inhibits cleavage and religation reactions of eukaryotic DNA topoisomerase I. Biochemistry 36 10777-10783... 

If we assume a common mechanism for the topoisomerase reactions illustrated in Figs. 2 and 3, then this mechanism must possess certain features. DNA binding and cleavage are clearly required and the positions of broken ends relative to another single- or double-stranded segment of DNA must somehow be altered before rejoining. As the product DNA is covalently closed, this break can only be transient and the enzyme must be capable of reforming the broken bond(s). Phosphodiester... 

From the foregoing sections, it is clear that all topoisomerase reaction mechanisms share several common features. After DNA binding, which in some cases organizes the DNA in a specific manner, DNA cleavage and the formation of a transient DNA-protein linkage ensue, followed by reformation of the broken phosphodiester bond(s). Reactions that must exist, but for which there is as yet little experimental evidence, are... 

In 2006, Delfoume et al. repotted the syntheses of two aza-analogs of wakayin and tsitsikammamines A and B based on a 1,3-dipolar cycloaddition reaction between the indole-4,7-dione 48 and a diazo-aminopropane derivative 49 (Scheme 15). One of the two analogs partially inhibits human topoisomerase I, whereas the synthetic intermediates inhibit the enzyme DNA cleavage activity at a concentration comparable to that of the control drug camptothecin [69, 70]. 

Helicases and topoisomerase are distinct in that topoisomerases alter the linking number of the dsDNA by phosphodiester bond cleavage and reunion, whereas helicases simply disrupt the hydrogen bonds that hold the two strands of DNA duplex together. This is accomplished in a reaction that is conpled with the hydrolysis of a NTP, therefore helicases are also nncleoside-5 -triphosphatases. Some hehcases unwind not only DNA duplexes but also DNA-RNA hybrids and RNA dnplexes (Matson and Kaiser-Roger, 1990). The nnwinding of dsDNA may proceed in a 5 —> 3 direction (e.g. DnaB, E. coli helicases I and 111, and monse ATPase B) or a 3 —> 5 direction (e.g. E. coli helicases 11 and IV). 

Fig. 1. Chemical reactions catalyzed by DNA topoisomerases. An initial transesterilication involves the attack of the nucleotide phosphorus by the tyrosine of the enzyme active site. This reaction produces cleavage of the phosphodiester bond and formation of a covalent link between the tyrosine and the DNA end (in the example, the 5 end). A second transesterilication, the attack of the phosphorus by the free hydroxyl DNA end, reverses the reaction, resealing the phosphodiester bond and liberating the tyrosine.

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