Daunomycin molecules, intercalated

The anticancer activity of daunomycin (34) (O Scheme 14) is attributed to the intercalation of the drug with DNA. This pattern of effect is common to all anthracyclines [46]. Two daunomycin molecules intercalate at each of the two C G sites at either site of the duplex d(CGTACG). This binding results in an increase in base pair-separation from 3.4 to 6.8 A as the molecule associates, which in turn leads to an unwinding of the helix and the formation of a noncovalent complex with the DNA. This results in the inhibition of DNA replication and RNA transcription [47]. 

The effects of intercalators (see also p. 262) are illustrated here using the example of the daunomycin-DNA complex, in which two daunomycin molecules (red) are inserted in the double helix (blue). The antibiotic s ring system inserts itself between G/C base pairs (bottom), while the sugar moiety occupies the minor groove in the DNA (above). This leads to a localized change of the DNA conformation that prevents replication and transcription. 

Antineoplastic Drugs. Cyclophosphamide (193) produces antineoplastic effects (see Chemotherapeutics, anticancer) via biochemical conversion to a highly reactive phosphoramide mustard (194) it is chiral owing to the tetrahedral phosphoms atom. The therapeutic index of the (3)-(-)-cyclophosphamide [50-18-0] (193) is twice that of the (+)-enantiomer due to increased antitumor activity the enantiomers are equally toxic (139). The effectiveness of the DNA intercalator dmgs adriamycin [57-22-7] (195) and daunomycin [20830-81-3] (196) is affected by changes in stereochemistry within the aglycon portions of these compounds. Inversion of the carbohydrate C-1 stereocenter provides compounds without activity. The carbohydrate C-4 epimer of adriamycin, epimbicin [56420-45-2] is as potent as its parent molecule, but is significandy less toxic (139). 

The effect of the position of side chains on the intercalation kinetics of anthra-quinones,101 which are related to the aromatic moiety of daunomycin (13), was studied with the stopped flow SDS sequestration technique. Guest molecules 14—17 can have two different intercalation modes, a classic mode where both side chains are located in the same groove of the DNA helix (14 and 16) or a threading mode where the side chains are located in opposite grooves of the DNA (15 and 17) (Scheme 7). The relative position of intercalated 14 with respect to the DNA bases was suggested to be the same as for 13. 

Perhaps a bit more subtle than those agents that react chemically with DNA are those that insert themselves between the stacked bases of the DNA double helix— intercalation. This alters the regular structure of the DNA molecule and may lead, for instance, to inhibition of mRNA synthesis. The structures of the intercalcating agents are generally quite complex and I will spare you the complexity. However, three names may be familiar—dactinomycin (Actinomycin D), daunorubicin (daunomycin), and doxorubicin (Adriamycin)— and intercalation is how they work. All three are natural products and were isolated from the fermentation broths of Streptomyces species. 

Figure 5-23 Stereoscopic drawing showing a molecule of daunomycin (Fig. 5-22) intercalated between two base pairs in a molecule of double-helical DNA, d(CGTACG). Nitrogen and oxygen atoms are shown as dots. From Quigley et al.220 Both daunomycin and adriamycin (doxorubicin 14-hydroxy-daunomycin) are important but seriously toxic anticancer drugs.

Daunorubicin (Daunomycin and Cerubidine) and doxorubicin (Adriamycin) bind to and cause the intercalation of the DNA molecule, thereby inhibiting DNA template function. They also provoke DNA chain scission and chromosomal damage. Daunorubicin is useful in treating patients with acute lymphocytic or acute granulocytic leukemia. Adriamycin is useful in cases of solid tumors such as sarcoma, metastatic breast cancer, and thyroid cancer. These agents cause stomatitis, alopecia, myelosuppression, and cardiac abnormalities ranging from arrhythmias to cardiomyopathy. 

Daunorubicin (Daunomycin and Cerubidine) and doxorubicin (Adriamycin) bind to and cause the intercalation of the DNA molecule, thereby inhibiting DNA template function. They also provoke DNA chain scission and chromosomal damage. 

The intercalation process has been the subject of extensive thermodynamic studies [3,4], providing free energy, entropy and enthalpy differences between the intercalated and free states of various drug molecules. On the other hand, dynamic studies are far less common. Some different aspects of the intercalating molecules have been studied using ultrafast methods [5]. Kinetic studies of drug intercalation are few in number, and a consensus on the mechanism has not been reached [6,7]. Thus, Chaires et al. [6] have proposed a three step model for daunomycin intercalation from the stopped flow association, while Rizzo et al. [7] have proposed a five step kinetic model. 

In all the crystal structures of anthracycline-DNA complexes, the drug molecule is intercalated at the CpG steps. A common feature of the more simple anthracycline antibiotics such as daunomycin and adriamycin is the aglycone aromatic system. 

Although a DNA molecule is heavily solvated by water (and ions), a detailed study of the role of water in various biological functions of DNA has yet to be carried out. However, some progress has recently been made towards understanding the role of water in the intercalation of anti-tumor dmgs (such as daunomycin, actinomycin, and cisplatin see Figure 7.4) into DNA. This is an important problem from a medical point of view and at the same time the microscopic aspects turned out to be quite interesting. 

The structures and dynamics of water molecules in the DNA grooves play an important role in the biological function of DNA. As discussed later, the intercalation of the anti-cancer drug daunomycin into DNA is indeed facilitated by water molecules in the grooves. While the role of water molecules in stabilizing a DNA duplex is well known (water molecules screen the electrostatic repulsion between the negatively charged phosphate ions, form HBs with the polar atoms of the nucleic... 

The term "intercalation" was first described in 1982 and it was found that intercalators shows a high affinity to double-stranded DNA structures because they prefer to locate between two adjacent pairs of bases [38], Intercalator molecules usually have planar aromatic rings, for example, some antibiotics such as daunomycin destroy deoxyribose-phosphate structure. These molecules are stabilized by r-bonds with bases [39],... 

Complexes of DNA with a drug doxorubicin (also known as adriamycin or hydroxydaunorubi-cin), Dox, used in cancer chemotherapy were studied using the NMR spectroscopy. Dox is an anthracycline antibiotic closely related to natural daunomycin and like all anthracyclines, it works by intercalating DNA. The intercalation of DNA by Dox (Figures 6.71b, 6.72, and 6.73) affects the behavior of bound water. The used concentration of Dox provides interaction of a large number of Dox molecules with each DNA macromolecule. Dox molecules are located in the places occupied by WAW in the slits between neighboring nucleotide planes. 

The chemical reduction of Fe(CN)g was identified as a reaction that would be catalyzed by electrochemically reduced MB intercalated within a DNA film. This electrocatalytic process is thermodynamically favored by 0.6 eV. Indeed, in the absence of MB, no signal is obtained for the anionic probe at a DNA-modified electrode, presumably because of electrostatic repulsion. In addition, the association of MB with the DNA film produces currents corresponding to the reduction of 1.4 molecules per immobilized duplex (Figure 8). However, when both MB and Fe(CN)g " are present in solution, irreversible electrochanical signals corresponding to multiple turnovers of the intercalated catalyst are observed. Only low levels of electrocatalysis were obtained when daunomycin was used as the intercalated species this probe binds DNA with higher affinity and may have slower exchange dynamics or solvent accessibility. 

Examples of nonnucleoside drugs which inhibit DNA synthesis by binding to the DNA double-helix include the acridines (e.g., proflavine) and various antibiotics (e.g. mitomycin C, adriamycin, daunomycin). The ability of the acridines to bind to DNA and RNA has led to their use as biological stains for these molecules. Binding is achieved by intercalation the planar ring system of proflavine, for example, intercalates (squeezes) between the stacked base pairs of the double-helix. Such a sandwich of DNA with bound molecules would be expected to geometrically distort (i.e., lengthen) the doublehelical structure this has been observed. 

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