**6. Rational for drug design**

When a compound intercalates into nucleic acids, there are changes, which occur in both the DNA and the compound during complex formation that can be used to study the ligand DNA interaction. The binding is of course an equilibrium process because no covalent bond formation is involved. The binding constant can be determined by measuring the free and DNA bound form of the ligand. In addition, DNA double helix structures are found to be more stable with intercalating agents present and show a reduced heat denaturation. Correlating these biophysical parameters with cytotoxicity is used to support the antitumor activity of these drugs as based on their ability to intercalate in DNA double helical structures. [15].

Improvement of anticancer drugs based on intercalating activity is not only focused on DNA-ligand interaction, but also on tissue distribution and toxic side effects on the heart (cardiac toxicity) due to redox reduction of the aromatic rings and subsequent free radical formation. Free radical species are thought to induce destructive cellular events such as enzyme inactivation, DNA strand cleavage and membrane lipid peroxidation [16, 17].

#### **7. Cisplatin-DNA interactions**

Cisplatin (cis-[PtCl2(NH3)2]) is the most widely used anticancer drug today. Since the development of cisplatin became one of the main biological targets for the antitumor compounds. It is used against ovarian, cervical, head and neck, esophageal and non-small cell lung cancer. However, chemotherapy treatment by cisplatin comes with a price of severe side effects including nausea, vomiting and ear damage, as cisplatin not only attacks cancer cells, but also healthy cells. It is therefore important to elucidate the details of the cisplatin mode of action to design new cisplatin analogs that specifically target cancer cells. Furthermore, most cancer cells are insensitive towards cisplatin or develop resistance. There is therefore, also a need for cisplatin analogues with a broader range of cytotoxicity. The search for new analogues and the elucidation of the complete mode of action have been going on for more than 40 years and there is an enormous amount of data available for researchers. Still, the picture of how cisplatin works is incomplete [11, 18].

**81**

it from QDs.

*Anticancer Drugs' Deoxyribonucleic Acid (DNA) Interactions*

Cellular DNA has been shown to be the primary target for cisplatin, although cisplatin can react with several other cellular components. In the cell, the salt concentration is significantly lower (~20 mM) and cis-[PtCl2(NH3)2] is hydrolyzed by high salt concentration (>100 mM) to the probable active

*The structure of the most common binding sites on the nucleobases for Pt. The big arrow on guanine indicates the overall favorable coordination site in DNA, the arrow towards thymine is dotted because the proton has to* 

preferentially to guanine N7> > adenine N7 > cytosine N3, first as a monoadduct, then forming a bidentate adduct. The primary products are 1,2-intrastrand cross-links of GpG (60–65%) or ApG (20–25%) sequences. A smaller amount corresponds to 1,3-intrastrand or G N7–G N7 interstrand adducts. The most common binding sites on the nucleobases for Pt are shown in **Figure 6** [18]. The big arrow on guanine indicates the overall favorable coordination site in DNA, the arrow towards thymine is dotted because the proton has to be

The formation of these 1,2-intrastrand cross-links alters the duplex conformation. The most dramatic effect is unwinding of the two strands and bending of the DNA double helix (several values for the bend angle are reported in the range 20–80°). The platinated adducts are assumed to be recognized by proteins, followed either by stabilization of the distorted DNA structure or removal of the lesion through repair [18]. The deformation of the DNA structure can interfere with the normal functions of DNA, such as replication and transcription, leading to cellular death by apoptosis or necrosis. The ineffective isomer of cisplatin, transplatin (trans-[PtCl2(NH3)2]), is not able to form 1,2-intrastrand cross-links [19]. Transplatin forms only 1,3-intrastrand and interstrand cross-links and this might be

In addition, a sensing system based on the photoinduced electron transfer of quantum dots (QDs) was also designed to measure the interaction of anticancer drug and DNA, taking mitoxantrone (MTX) as a model drug. The MTX adsorbed on the surface of QDs and this, can quench the photoluminescence (PL) of QDs through the photoinduced electron-transfer process, then the addition of DNA will bring the restoration of QDs PL intensity, as DNA can bind with MTX and remove

. The hydrolyzed product binds to DNA and

+

*DOI: http://dx.doi.org/10.5772/intechopen.85794*

species cis-[PtCl(OH2)(NH3)2]

*be removed before Pt association.*

**Figure 6.**

removed before Pt association.

the reason why transplatin is antitumor inactive [18].

*Anticancer Drugs' Deoxyribonucleic Acid (DNA) Interactions DOI: http://dx.doi.org/10.5772/intechopen.85794*

#### **Figure 6.**

*Biophysical Chemistry - Advance Applications*

**6. Rational for drug design**

*Structure of hairpin polyamide Im-Py-Py.*

**Figure 5.**

membrane lipid peroxidation [16, 17].

**7. Cisplatin-DNA interactions**

expelled from the cell-by-cell membrane transport proteins that commonly referred

When a compound intercalates into nucleic acids, there are changes, which occur in both the DNA and the compound during complex formation that can be used to study the ligand DNA interaction. The binding is of course an equilibrium process because no covalent bond formation is involved. The binding constant can be determined by measuring the free and DNA bound form of the ligand. In addition, DNA double helix structures are found to be more stable with intercalating agents present and show a reduced heat denaturation. Correlating these biophysical parameters with cytotoxicity is used to support the antitumor activity of these drugs as based on their ability to intercalate in DNA double helical structures. [15]. Improvement of anticancer drugs based on intercalating activity is not only focused on DNA-ligand interaction, but also on tissue distribution and toxic side effects on the heart (cardiac toxicity) due to redox reduction of the aromatic rings and subsequent free radical formation. Free radical species are thought to induce destructive cellular events such as enzyme inactivation, DNA strand cleavage and

Cisplatin (cis-[PtCl2(NH3)2]) is the most widely used anticancer drug today. Since the development of cisplatin became one of the main biological targets for the antitumor compounds. It is used against ovarian, cervical, head and neck, esophageal and non-small cell lung cancer. However, chemotherapy treatment by cisplatin comes with a price of severe side effects including nausea, vomiting and ear damage, as cisplatin not only attacks cancer cells, but also healthy cells. It is therefore important to elucidate the details of the cisplatin mode of action to design new cisplatin analogs that specifically target cancer cells. Furthermore, most cancer cells are insensitive towards cisplatin or develop resistance. There is therefore, also a need for cisplatin analogues with a broader range of cytotoxicity. The search for new analogues and the elucidation of the complete mode of action have been going on for more than 40 years and there is an enormous amount of data available for researchers. Still, the picture of how cisplatin works is incomplete [11, 18].

to as ABC transporters or ATP binding cassette proteins [14].

**80**

*The structure of the most common binding sites on the nucleobases for Pt. The big arrow on guanine indicates the overall favorable coordination site in DNA, the arrow towards thymine is dotted because the proton has to be removed before Pt association.*

Cellular DNA has been shown to be the primary target for cisplatin, although cisplatin can react with several other cellular components. In the cell, the salt concentration is significantly lower (~20 mM) and cis-[PtCl2(NH3)2] is hydrolyzed by high salt concentration (>100 mM) to the probable active species cis-[PtCl(OH2)(NH3)2] + . The hydrolyzed product binds to DNA and preferentially to guanine N7> > adenine N7 > cytosine N3, first as a monoadduct, then forming a bidentate adduct. The primary products are 1,2-intrastrand cross-links of GpG (60–65%) or ApG (20–25%) sequences. A smaller amount corresponds to 1,3-intrastrand or G N7–G N7 interstrand adducts. The most common binding sites on the nucleobases for Pt are shown in **Figure 6** [18]. The big arrow on guanine indicates the overall favorable coordination site in DNA, the arrow towards thymine is dotted because the proton has to be removed before Pt association.

The formation of these 1,2-intrastrand cross-links alters the duplex conformation. The most dramatic effect is unwinding of the two strands and bending of the DNA double helix (several values for the bend angle are reported in the range 20–80°). The platinated adducts are assumed to be recognized by proteins, followed either by stabilization of the distorted DNA structure or removal of the lesion through repair [18]. The deformation of the DNA structure can interfere with the normal functions of DNA, such as replication and transcription, leading to cellular death by apoptosis or necrosis. The ineffective isomer of cisplatin, transplatin (trans-[PtCl2(NH3)2]), is not able to form 1,2-intrastrand cross-links [19]. Transplatin forms only 1,3-intrastrand and interstrand cross-links and this might be the reason why transplatin is antitumor inactive [18].

In addition, a sensing system based on the photoinduced electron transfer of quantum dots (QDs) was also designed to measure the interaction of anticancer drug and DNA, taking mitoxantrone (MTX) as a model drug. The MTX adsorbed on the surface of QDs and this, can quench the photoluminescence (PL) of QDs through the photoinduced electron-transfer process, then the addition of DNA will bring the restoration of QDs PL intensity, as DNA can bind with MTX and remove it from QDs.

**Figure 7.** *Assumed mechanism for the formation of cisplatin-DNA adducts.*

Cisplatin-DNA sequence selectivity has been given great attention from the research community. Several studies show that cisplatin first binds monofunctionally to guanine N7 and is particularly reactive towards Gn-runs (n ≥ 2) (**Figure 7**) [18, 20, 21]. The high nucleophilicity of Gn-runs attracts the positively charged cisplatin monoaqua specie. The lifetime of the monoadduct is relatively long and it has therefore been suggested that the initial monoadduct is crucial for the type of cross-linked adduct formed and thus for the cytotoxic properties of the Pt complex. The main factors influencing the mono-functional binding affinity in DNA are thought to be [18] the type of bound nucleotide and of the adjacent residues, the steric effects of the Pt complex, the hydrogen binding properties of the Pt-DNA adduct and the DNA conformation.

### **8. Sequence specific structural perturbation**

The formation of a cisplatin adduct with the GpG bases requires a significant tilting of the bases leading to a perturbation of the regular B-DNA conformation. The structural perturbation has been shown to be specifically recognized by a number of cellular proteins, including proteins with high-mobility group (HMG) binding domains and the TATA box binding protein [22]. It is believed that (some of) these recognition proteins mediate the cellular response which finally induces cell death by apoptosis or necrosis. In some cases, relatively subtle changes in the adduct structure can affect the recognition and the biological effects in a major way. This is exemplified by the cisplatin analogue oxaliplatin which forms similar G\*G\*-Pt adducts as cisplatin [18]. However, the oxaliplatin-G\*G adducts differ in repair efficiency, mutagenesis and translesion synthesis, believed to be related to the differential activity of the two drugs (oxaliplatin is used, in combination with 5-fluorouracil, for the treatment of colorectal cancers against which cisplatin is inactive). The evaluation of the structural details of the platinum-DNA adducts and of their effects on protein, recognition can therefore help to understand why the biological activities of two similar platinum compounds (e.g., cisplatin versus oxaliplatin) are different. So far only nine cisplatin-DNA adducts have been characterized by NMR and/or x-ray crystallography. These structures were extensively reviewed by Ano et al. and found to be basically similar in structure. The cisplatin-GG adduct kinks the double helix approx. Approximately 60 towards the major groove and induces N sugar pucker for X of 5′ XG\*, 5′ G\* and the C complementary to 3′ G\* [18].

**83**

**Figure 8.**

*Schematic interaction between DNA and mitomycin-C.*

*Anticancer Drugs' Deoxyribonucleic Acid (DNA) Interactions*

therefore inhibiting single strand formation [8].

comprised between the chromophores (**Figure 9**) [8].

This metal-based compound or coordination compounds that bind to DNA have been an active area of research since the discovery of cisplatin and the platinum-based drugs. The transition-metal compounds bind to DNA through several ways and different factors that promote it, such as the intercalant ligand and the nature and position of the substituent over it. Several techniques to follow metal-based drugs interactions with DNA are used as a powerful tool in order to reach a deep knowledge of the param-

DNA damaging agents (drugs that interfere with DNA function by chemically

Mitomycin-C is a well-characterized antitumor antibiotic that forms a covalent interaction with DNA after reductive activation (**Figure 8**). The activated antibiotic forms a cross-linking structure between guanine bases on adjacent strands of DNA

Several studies have proved that both echinomycin quinoxaline rings bisintercalate into DNA, with CG selectivity, while the inner part of the depsipeptide establishes H-bonds with the DNA bases of the minor groove region of the two base pairs

eters involved in the stabilization of coordination compound-DNA adduct.

**9. Methods for elucidation of DNA-anticancer drug interactions**

modifying specific nucleotides) includes mitomycin-C and echinomycin.

*DOI: http://dx.doi.org/10.5772/intechopen.85794*

**9.1 Mitomycin-C**

**9.2 Echinomycin**

This metal-based compound or coordination compounds that bind to DNA have been an active area of research since the discovery of cisplatin and the platinum-based drugs. The transition-metal compounds bind to DNA through several ways and different factors that promote it, such as the intercalant ligand and the nature and position of the substituent over it. Several techniques to follow metal-based drugs interactions with DNA are used as a powerful tool in order to reach a deep knowledge of the parameters involved in the stabilization of coordination compound-DNA adduct.
