1. health and fitness
2. disease
3. cancer

Chapter I
INTRODUCTION
Cancer is a class of diseases or disorders characterized by uncontrolled/
abnormal division of cells and the ability of these to spread, either by direct growth
into adjacent tissue, or by implantation into distant sites by metastasis, in which
cancer cells are transported through the bloodstream or lymphatic system. The
abnormal cellular division of this is not subject to normal growth controls.1 It is one
of the most dreadful diseases due to incurable affliction that insidiously attacks
people of all cultures and ages. While, cancer is an ancient disease, the inability to
cure cancer has persisted despite impressive advances in scientific knowledge and
medical techniques.
Though treatment remained the same, in the 16th and 17th centuries it
became more acceptable for doctors to dissect bodies to discover the cause of death.
The German prof. Wilhelm Fabry believed that breast cancer was caused by a milk
clot in a mammary duct and the Dutch prof. Francocis de la, believed that this
disease was the outcome of chemical processes, and that acidic lymph fluid was the
cause of cancer. His contemporary Nicolaes Tulp believed that cancer was a poison
that slowly spreads, and concluded that it was contagious.2 In the 18th century, it
was discovered that the 'cancer poison' spread from the primary tumour through
the lymph nodes to other sites (metastasis). The use of surgery to treat cancer had
poor results due to problems with hygiene. The renowned Scottish surgeon
Alexander Monro saw only two breast tumour patients out of 60 surviving surgery
for two years. In the 19th century, asepsis (practice to reduce contaminants)
improved surgical hygiene and as the survival statistics went up, surgical removal
of the tumour became the primary treatment for cancer. When Marie Curie and
Pierre Curie discovered radiation at the end of the 19th century, they stumbled
upon the first effective non-surgical cancer treatment. The radiotherapy also the first
signs of multi-disciplinary approaches to cancer treatment. The improvement in
surgical reflects in diagnosing at an earlier and improvements in treatment. Cancer
1
Chapter I
is presently responsible for about 25% of all deaths3 and on a yearly basis, 0.5% of
the population is diagnosed with cancer.
NOMENCLATURE
The following terms may be used to designate abnormal growths:

Neoplasia and neoplasm are the scientific designations for cancerous diseases. This
group contains a large number of different diseases. Neoplasms can be benign or
malignant.

Cancer is a widely used word that is usually understood as synonymous with
malignant neoplasm. It is occasionally used instead of carcinoma, a sub-group of
malignant neoplasms.

Because of its overwhelming popularity relative to 'neoplasia', it is used
frequently instead of 'neoplasia', even by scientists and physicians, especially
when discussing neoplastic diseases as a group.

Tumour in medical language simply means swelling or lump, either neoplastic,
inflammatory or other. In common language, however, it is synonymous with
'neoplasm', either benign or malignant. This is inaccurate since some neoplasms
do not usually form tumours, for example leukemia or carcinoma.

Paraneoplasia is a disturbance associated with a neoplasm but not related to the
invasion of the primary or a secondary tumour. Disturbances can be hormonal,
neurological, hematological, biochemical or otherwise clinical.
TYPES OF TUMOURS
There are over 200 different cancers. The various types of cancer are classified4
by the type of cell that resembles the tumour and, therefore, the tissue presumed to
be the origin of the tumour. The following general categories are usually accepted:

Carcinoma: malignant tumours derived from epithelial cells. This group
represents the most common cancers, including the common forms of breast,
prostate, lung and colon cancer.
2
Chapter I

Lymphoma and leukemia: malignant tumours derived from blood and bone
marrow cells.

Sarcoma: malignant tumours derived from connective tissue, or mesenchymal
cells.

Mesothelioma: tumours derived from the mesothelisal cells lining the
peritoneum and the pleura.

Glioma: tumours derived from glia, the most common type of brain cell.

Germinoma: tumours derived from germ cells, normally found in the testicle
and ovary.

Choriocarcinoma: malignant tumours derived from the placenta.
Malignant tumours are usually named using the Latin or Greek root of the organ
as a prefix and the above category name as the suffix. For instance, a malignant
tumor of liver cells is called hepatocarcinoma; a malignant tumour of the fat cells is
called liposarcoma. For common cancers, the English organ name is used. For
instance, the most common type of breast cancer is called ductal carcinoma of the
breast or mammary ductal carcinoma. Here, the adjective ductal refers to the
appearance of the cancer under the microscope, resembling normal breast ducts.
Benign tumours are named using -oma as a suffix with the organ name as the root.
For instance, a benign tumour of the smooth muscle of the uterus is called
leiomyoma and the common name is fibroid.
FACTORS RESPONSIBLE FOR CANCER
Cancer causing factors5 have been classified into three major groups include
physical, viral and chemical carcinogens.
Physical carcinogens include hard and soft X-rays, UV light, asbestos fibres and many
other external agents.
Viral carcinogens, which for decades were considered not to cause cancer but simply
take advantage of a weakened cell, have been positively linked to the onset of
specific cancers. Birkett's lymphoma, among Africans and South East China have
3
Chapter I
been found to be caused by the Epstein-Barr virus. Cervical cancer is also believed
to be associated with the Herpes Simplex Virus Type II, and certain leukemias and
lymphomas are caused by the Human T-cell Leukemia virus.
Chemical carcinogens are believed to be by far the greatest cause of cancer. They are
substances that interact directly or indirectly with DNA, causing changes in the
genetic code.
TREATMENT OF CANCER
Cancer can be treated by surgery, chemotherapy, radiation therapy,
immunotherapy, monoclonal antibody therapy or other methods. The choice of
therapy depends upon the location and grade of the tumour and the stage of the
disease, as well as the general state of the patient. A number of experimental cancer
treatments are also under development. Complete removal of the cancer without
damage to the rest of the body is the goal of treatment.
1. SURGERY
In theory, cancers can be cured if entirely removed by surgery, but this is not
always possible. When the cancer has metastasized to other parts in the body prior
to surgery, complete surgical excision is usually impossible. Examples of surgical
procedures for cancer include mastectomy for breast cancer and prostatectomy for
prostate cancer.
2. MONOCLONAL ANTIBODT THERAPY
Immunotherapy is the use of immune mechanisms against tumours. These
are used in various forms of cancer, such as breast cancer (trastuzumab/Herceptin)
and leukemia (gemtuzumab ozogamicin/ Mylotarg). The agents are monoclonal
antibodies directed against proteins that are characteristic to the cells of the cancer
in question, or cytokines that modulate the immune system's response.
3. IMMUNOTHERAPHY
Other, more contemporary methods for generating non-specific immune
response against tumours include intravesical Bacille Calmette-Guerin (BCG)
4
Chapter I
immunotherapy for superficial bladder cancer, and use of interferon and
interleukin. Vaccines to generate non-specific immune responses are the subject of
intensive research for a number of tumours, notably malignant melanoma and renal
cell carcinoma.
4. RADIATION THERAPHY
Radiation therapy also called as radiotherapy, X-ray therapy, or irradiation is
the use of ionizing radiation to kill cancer cells and shrink tumours. Radiation
therapy can be administered externally via external beam radiotherapy (EBRT) or
internally via brachytherapy. Radiation therapy injures or destroys cells in the area
being treated by damaging their genetic material, and enables to grow and divide.
5. HORMONAL SUPPRESSION
The growth of some cancers can be inhibited by providing or blocking certain
hormones. Common examples of hormone-sensitive tumours include certain types
of breast and prostate cancers. Removing or blocking estrogen or testosterone is
often an important additional treatment.
6. CHEMOTHERAPHY
Chemotherapy is the treatment of cancer with drugs that can destroy cancer
cells by impeding their growth and reproduction. The first drug used for cancer
chemotherapy was not originally intended for that purpose. Mustard gas was used
as a chemical warfare agent during World War I and was studied further during
World War II. During a military operation in World War II, a group of people were
accidentally exposed to mustard gas and were later found to have very low white
blood cell (WBC) counts. It was reasoned that an agent that damaged the rapidly
growing WBC might have a similar effect on cancer. Therefore, in the 1940s, several
patients with advanced lymphomas were given the drug by vein, rather than by
breathing the irritating gas. Their improvement, although temporary, was
remarkable. That experience led researchers to look for other substances that might
5
Chapter I
have similar effects against cancer. As a result, many other drugs have been
developed to treat cancer, and drug development since then has exploded into a
multi-billion dollar industry. The targeted-therapy revolution has arrived, but the
principles and limitations of chemotherapy discovered by the early researchers still
apply.
Cancer treatment will be entirely based on person’s unique situation. Certain
types of cancer respond very differently to a various types of treatment, so
determining the type of cancer is a vital step toward knowing which treatments will
be the most effective. The cancer's stage will also determine the best course of
treatment, since early-stage cancers respond to different therapies than later-stage
ones. Person’s overall health, lifestyle, and personal preferences will also play a part
in deciding which treatment options will be best.
Although chemotherapeutic drugs attack reproducing cells, they cannot
differentiate between reproducing cells of normal tissues and cancer cells. The
damage to normal cells can result in side effects. These cells usually repair
themselves after chemotherapy. Several exciting uses of chemotherapy hold more
promise for curing or controlling cancer. New drugs, new combinations of
chemotherapy drugs and new delivery techniques are the expected advances in the
coming years for curing or controlling cancer and improving the quality of life for
people with cancer.
Chemotherapeutic drugs are divided into several categories based on how
they affect specific chemical substances within the cancer cells, which cellular
activities or processes the drug interferes with, and which specific phases of the cell
cycle the drug affects. These include DNA interactive agents, DNA topoisomerase I
and II inhibitors, carbonic anhydrase (CA) inhibitors, CDK inhibitors, tubulin
polymerization inhibitors, antimitotic agents, antimetabolites, and miscellaneous
agents.
6
Chapter I
TYPES OF CHEMOTHERAPHY DRUGS
Chemotherapy drugs are divided into several groups based on how they
affect specific chemical substances within cancer cells, which cellular activities or
processes the drug interferes with, and which specific phases of the cell cycle the
drug affects.
ALKYLATING AGENTS
These agents directly damage DNA to prevent the cancer cell from
reproducing. As a class of drugs, these agents are not phase-specific and in other
words, they work in all phases of the cell cycle.
NITROSOUREAS
Nitrosoureas act in a similar way to alkylating agents. They interfere with
enzymes that help copy and repair DNA. They, too, are not phase specific. Unlike
many other drugs, these agents are able to travel from the blood to the brain, so they
are often used to treat brain tumours.
ANTIMETABOLITES
These are a class of drugs that interfere with DNA and RNA growth. These
agents damage cells during the S phase and are commonly used to treat leukemias,
tumours of the breast, ovary, and the gastrointestinal tract, as well as other cancers.
ANTHRACYCLINES AND RELATED DRUGS
Anthracyclines are antitumour antibiotics that interfere with enzymes
involved in DNA replication. These agents work in all phases of the cell cycle. Thus,
they are widely used for a variety of cancers.
7
Chapter I
TOPOISOMERASE INHIBITORS
TOPOISOMERASE INHIBTORS
These drugs interfere with enzymes called topoisomerases, which are
important in accurate DNA replication. They are used to treat certain leukemias, as
well as lung, ovarian, gastrointestinal, and other cancers.
MITOTIC INHIBITORS
Mitotic inhibitors are plant alkaloids and other compounds derived from
natural products. They can stop mitosis or inhibit enzymes from making proteins
needed for reproduction of the cell. These work primarily during the M phase of the
cell cycle but can cause cellular damage in all phases.
CORTICOSTERI HORMONES
Steroids are natural hormones and hormone-like drugs that are useful in
treating some types of cancer such as lymphoma, leukemias, and multiple myeloma
as well as other illnesses. When these drugs are used to kill cancer cells or slow their
growth, they are considered chemotherapy drugs.
DNA AS A CELLULAR TARGET FOR CHEMOTHERAPEUTIC AGENTS
DNA has been considered a favored target for cancer chemotherapeutic
agents. Indeed, many of the most effective clinical agents, such as alkylating and
intercalating agents, are DNA interactive. Achieving the desired sequence
specificity with DNA-interactive agents is considered to be one of the most
formidable hurdles in the development of new agents to achieve therapeutic
invention.
The double helical structure of deoxyribonucleic acid (DNA) represents the
richest source of information within a living organism. Importantly, its sequence
codes not only for protein/enzyme synthesis via the process of translation, but it
also codes for RNA synthesis, which, in light of the discovery of ribozymes, is likely
to play a much larger cellular role than previously believed.6
8
Chapter I
The structure of DNA (Fig. 1) was established by James Watson and Francis
Crick in 1953.7 It consists of two ant parallel strands composed of the nucleotides
adenine (A), thymine (T), guanine (G) and cytosine (C), supported on a sugar
phosphate backbone. The nucleotides form unique hydrogen bonded pairs (purine
with pyrimidine), AT and GC (Fig. 2). Besides the hydrogen bonds between the
nucleotides, the double helix is stabilized by electrostatic interactions, vander Waals
interactions,
complex
hydration/dehydration
contributions
composed
of
hydrophobic component, solvation electrostatics. The particular order of the bases
that are arranged along the sugar-phosphate backbone is called the DNA sequence;
the sequence specifies the exact genetic instructions required to create a particular
organism with its own unique traits.
There are three helical forms of DNA (A, B and Z) that differ with respect to
various parameters that describe their three-dimensional structure. However, Bform DNA is the most common one and is more stable under high humidity
conditions because water molecules stabilize the structure by forming a spine of
hydration in the minor groove.8
Figure 1. Structure of DNA.
9
Chapter I
Thymine
Cytosine
N
O
Sugar
N
N
H
H
H
N
H
N
Adenine
O
O
N
N
O
Sugar
H
H
N
Sugar
H
N
N
N
H
N
N
N
Sugar
Guanine
N
Figure 2. Hydrogen bonding between A-T and G-C base pairs of DNA.
In B-DNA, the GC and AT base pairs are stacked in a right-handed double
helix, and are hydrogen bonded to one another. Because each base pair contains one
two-ringed purine (A or G) and one single-ringed pyrimidine (T or C), the width of
each base pair is similar contributing to the smooth cylindrical shape of the double
helix. The base pairs are rotated by 36° with respect to each adjacent pair, so that
there are 10 pairs per helical turn, each separated by 3.4 Å. This gives rise to two
well-defined channels known as the minor and major grooves. The major groove is
approximately 24 Å in width and much deeper than minor groove, which is only 10
Å in width.9 Due to it’s predominate form, B-DNA is used in the design of new
DNA-binding antitumour drugs.
EVALUATION OF DRUG-DNA INTERACTIONS
Understanding the forces involved in the binding of proteins or small
molecules to DNA is of prime importance due to two major reasons. Firstly, the
design of sequence specific drugs having requisite affinity for DNA requires a
knowledge how the structure of the drug is related to the specificity/affinity of
binding and what structural modifications could result in a drug with desired
qualities. Secondly, identifying the forces/energetics involved in such processes is
fundamental to unraveling the mystery of molecular recognition in general and
DNA binding in particular.
10
Chapter I
In recent years, several advances have been made in the elucidation of drugDNA interactions. Spectral methods are available to evaluate the extent of DNAbinding and to know in which sequence the ligand binds. Physical methods like
UV-spectroscopy, fluorescence, circular dichorism (CD), optical rotatory dispersion
(ORD), IR, Raman spectroscopy and viscometry measurements have been used for
the measurement of binding.
Thermal denaturation studies on DNA are common and involve measuring
the melting point of DNA alone and in the presence of a ligand (drugs). Binding
will often stabilize the helix and elevate the melting temperature. However, none of
these physical techniques allows determining the specific location of binding on a
DNA strand. To do this two types of assays are used namely, strand cleavage assay
and affinity cleavage assay.10
Other powerful techniques for studying DNA binding with short lengths of
DNA includes NMR and X-ray crystallography,11 which can provide precise
structural information about functional groups involved. Three dimensional 1H, 31P
NMR experiments such as NOSEY or COSY can be used to locate precisely the
ligand on the strand and which can be used in conjugation with computational
methods to generate useful 3-dimensional models of ligand-DNA complexes. DNA
‘foot printing’ is an alternative approach that can be used for covalent and noncovalent binders, intercalaters and other type of adducts such as co-ordination
complexes and triple helices.12
TYPES OF DRUGS THAT INTERACT WITH DNA
The major groups of clinically important DNA reactive agents are covalent
and non-covalent binders.
1. NON-COVALENT BINDERS
INTERCALATORS
Intercalators are molecules that insert perpendicularly into DNA without
forming covalent bonds. The only recognized forces that maintain the stability of
11
Chapter I
the DNA–intercalators complex, even more than DNA alone, are van der Waals,
hydrogen bonding, hydrophobic, and/or charge transfer forces.13
In the early 1960s, Lerman14 conducted a number of physical studies on the
interactions of DNA with planar aromatic cations, and concluded that planar
aromatic molecules could bind to DNA by a process, which is termed as
intercalation. This mode of binding has now been established for a large number of
polycyclic aromatic systems which include amonafide and amsacrine (Fig. 3). There
are also bis-intercalators like bis-phenazines, which consist of two intercalating
moieties joined by a linker, capable of intercalation at two sites separated by a
distance defined by the linker length. Other class of intercalators include ethidium
bromide and mitoxantrone which is a simplified analogue of the anthracyclines that
is easily synthesized and has less toxic side effects, which display antitumour
activity by this mechanism.
H 3C
O
N
N
CH 3
H 3 CO
NHSO2 CH 3
H2 N
NH2
HN
O
NH2
Amonafide
N Br
CH3
N
Ethidium dibromide
Amsacrine
OH
NH
N
N
N
N
O
N
H
N
Me
N
H
HN
O
OH
HN
O
OH
O
Bis-phenazine
Mitoxantrone
NH
OH
Figure 3. DNA intercalators.
12
Chapter I
2. COVALENT BINDERS
ALKYLATORS
Alkylating agents were among the first anti-cancer drugs and are the most
commonly used agents in chemotherapy today. Alkylating agents act directly on
DNA, causing cross-linking of DNA strands, abnormal base pairing, or DNA strand
breaks, thus preventing the cell from dividing. These agents are generally
considered to be cell cycle phase nonspecific, meaning that they kill the cell in
various and multiple phases of the cell cycle. Although alkylating agents may be
used for most types of cancer, they are generally of greatest value in treating slowgrowing cancers. These are not as effective on rapidly growing cells. Examples of
alkylating
agents
include
cisplatin,15
nitrogen-mustards
(mechlorethamine,
chlorambucil)16 and ethylene amides, methane sulphonic acid esters, nitrosoureas,
triazenes (Fig. 4).
Figure 4. DNA alkylating agents.
3. DNA STRAND BREAKERS
Some DNA-interactive drugs initially intercalate into DNA but then in
certain conditions, react in such a way as to generate radicals. The reaction of these
radicals with the sugar moieties leads to DNA strand scission. e.g. bleomycin and
the enediyne antitumor antibiotics.17 In this category, recently discovered prodrug
Phortress 18 (under clinical trials) included which acts by a novel mechanism of AhR
(aryl hycrocarbon receptor19) binding and subsequent release of electrophilic
intermediates which reacts with DNA in a lethal way leading to selective cell death
(Fig. 5).
13
Chapter I
Figure 5. DNA strand breakers
GROOVE BINDERS
Groove binding can be via either major or minor groove by covalently
(irreversible) or non-covalently (reversible). 20 It is believed that groove binders with
increased selectivity will produce a greater biological response for a given dose (and
hence cause fewer toxic side effects) than non-selective groove binders. Molecules
that target particular DNA sites also have the potential to be used for the selective
suppression of transcription from particular gene sequences.21
For many years the major groove was the focus of most studies aimed at
understanding sequence-specific DNA recognition. This emphasis grew largely out
of the belief that complementary networks of hydrogen bonds provide the primary
basis for specific DNA recognition. There are more hydrogen bond donors and
acceptors on the major groove edge of each base pair than on the minor groove
edge. There are, therefore, more opportunities for discriminating different base
pairs using hydrogen bonds from the major groove. In the minor groove, the
principal difference between base pairs is that G-C base pairs contain an exo-cyclic
amino group that protrudes into the groove. This amino group makes the steric and
electronic environment of the minor groove at G-C base pairs profoundly different
from that at A-T base pairs. Thus, while designing ligands to discriminate A-T-rich
and G-C-rich DNA sites in the minor groove seemed feasible, the potential for
achieving greater sequence discrimination was regarded by many as limited. This
picture of the potential for sequence-selective binding in the minor groove has
14
Chapter I
changed considerably in the past few years because of several developments. In
1989, Wemmer and colleagues showed that distamycin, the prototypical A-T
selective minor groove binder, can bind to DNA as an antiparallel dimer. This
unexpected finding forced a re-evaluation of the nature of A-T selectivity and the
role of a narrow minor groove in binding site selection. More importantly, the
finding raised new possibilities for the design of minor groove binders that are
selective for sequences containing mixed A-T and G-C base pairs, or for sequences
containing only G-C base pairs. Most of the DNA interactive proteins bind in the
major groove, while small molecules of less than 1000 Da, including many
antibiotics bind in the minor groove e.g. distamycin,22 netropsin,23 CC-1065,24
pyrrolo[2,1-c][1,4]benzodiazepines,25 Hoechst 33258,26 Mitomycin C 27 (Fig. 6).
Figure 6. Minor groove binders.
15
Chapter I
ENZYME INHIBITORS
Enzyme inhibitors are molecules that bind to enzymes and decrease their
activity. Since blocking an enzyme's activity can kill a pathogen or correct a
metabolic imbalance, many drugs are enzyme inhibitors. They are also used as
herbicides and pesticides. The binding of an inhibitor can stop a substrate from
entering the enzyme's active site and/or hinder the enzyme from catalysing its
reaction. Inhibitor binding is either reversible or irreversible. Irreversible inhibitors
usually react with the enzyme and change it chemically. Many drug molecules are
enzyme inhibitors, so their discovery and improvement is an active area of research
in biochemistry and pharmacology. A medicinal enzyme inhibitor is often judged
by its specificity or lack of binding to other proteins and its potency (its dissociation
constant, which indicates the concentration needed to inhibit the enzyme). A high
specificity and potency ensure that a drug will have few side effects and thus low
toxicity. Some of the example of enzymes wich play key role in cell division are
cyclin-dependent
kinase,
carbonic
anhydrase,
tubulin
polymerisation,
topoisomerase I and II etc.
CYCLIN-DEPENDENT KINASE (CDK)
The cyclin-dependent kinases (CDKs) are a family of serine/threonine
protein kinases that play a significant role in cell cycle division.28 In many forms of
cancer a deregulation of CDK function and consequent loss of cell cycle control are
observed. This suggests that the development of pharmacological inhibitors of
CDKs may be an anticancer strategy.29 Uncontrolled cell growth and proliferation
are hallmarks of all cancers and are directly linked to cell cycle dysregulation.
Cyclin-dependent kinase 2 (CDK2) in complex with cyclins E and/or A is a key cell
cycle regulator and continues to be an attractive target for the discovery of new
antitumor agents.30 Classically, the cell cycle is defined as the sequence of events
leading to the undisturbed division of a cell into two daughter cells. The exit of a
differentiated cell from the resting G0 phase is marked by the first gap (G1) phase
16
Chapter I
during which the cell prepares for DNA replication in the S phase. This is followed
by the second gap phase (G2) that precedes the mitosis. Cell cycle regulatory
proteins have been implicated previously in neuronal cell death.31 Cyclin A is
produced in the G1 phase, then expressed during the S and G2 phases, while the
expression of cyclin B is typically maximal during the G2–M phase transition and
controls the passage through the M phase by primarily associating with and
activating CDK2.32
3-Amino 9-thio (10H)-acridone and benzothiadiazines (Fig. 7) have inhibited
CDK4 kinase activity in vitro. The growth inhibitory effect of benzothiadiazines
against CDK4 is due to the partial competetion with ATP by binding to the ATPbinding pocket or by interfering with ATP binding.33
S
O
N
H
NH2
S
O
O
NH
N
O
N
N
Cl
C2H 5
F
HN
S
Figure 7. Aminothioacridone and benzothiadiazine exhibiting CDK4 inhibition.
Lin and co-workers34 reported triazole-diamine analogues as cyclindependent kinase inhibitors. These compounds showed potent and selective CDK1
and CDK2 inhibitory activities and exhibited IC50 values up to 2.1 nM.
S
H 2NO2S
O
F
N N
N
H
N
F
F
H 2NO2S
NH2
O
N
H
N
NH 2
Figure 8. Diamino triazole and pyridine inhibiting CDK .
17
Chapter I
CARBONIC ANHYDRASE (CA)
The carbonic anhydrase (CA) family of Zn (II) metalloenzymes catalyzes the
reversible hydration of CO2 to HCO3. These are involved in various physiological
processes associated with pH control, respiration, transport of CO2/HCO3 between
metabolizing tissues and the lungs, fluid secretion, biosynthetic reactions, such as
the lipogenesis, gluconeogenesis and ureagenesis. 35
Reactions catalyzed by carbonic anhydrase:
CO2
+
H 2O
HCO3 - + H +
CA
HCO3 - +
H 2CO3
CO 2 +
H+
H2O
(in tissues)
( in lungs)
There are fouteen different carbonic anhydrase isoforms have been identified
in mammals. It has been known for some time that several of these isozymes are
cytosolic (CA I, CAII, CA III, CA VII), CA IV is membrane-bound. CA V is present
only in mitochondria, and CA VI is secreted in saliva. The inhibition of CAs has
been exploited clinically for several decades for the treatment of a variety of
conditions including glaucoma, epilepsy, and gastric ulcers. More recently, CA
inhibition has been implicated as playing an important role in cancer progression.36
Generally, an aromatic or heteroaromatic sulfonamide moiety (ArSO2NH2) is the
primary recognition element necessary for small molecules to bind the active site of
CA. Coordination of the nitrogen atom of the ionized sulfonamide anion
(ArSO2NH-) to the active site Zn (II) of CA facilitates this protein-small molecule
interaction. Several classical clinical agents from this class of CA inhibitors include
acetazolamide
(AAZ),
methazolamide
(MZA),
ethoxazolamide
(EZA),
dichlorophenamide (DCP), brinzolamide (BRZ), dorzolamide (DZA) and indisulam
(IND) (Fig. 9) are in phase II clinical trials as an anticancer agent to treat solid
tumours.37
18
Chapter I
Figure 9. Sulfonamides inhibiting carbonic anhydrase.
TUBULIN POLYMERISATION
Microtubules (MTs), rigid and hollow cylindrical structures of about 25 nm
diameter, are composed of - and -tubulin dimers (Fig. 10). They determine cell
shape and play important roles in diverse processes such as cell division, cell
motility and migration, cellular transport, and signal transduction. Both  and tubulins exist in several isotypic forms and can undergo several post-translational
modifications. In higher eukaryotes at least 14 tubulin isotypes have been reported
that are expressed in a tissue specific manner. MTs are essential in a diverse array of
eukaryotic cell functions, such as mitosis, cell motility, and intracellular organelle
transport. Disruption of microtubule leads to cell cycle arrest at G2/M phase
followed by apoptotic cell death.38
19
Chapter I
Figure 10. Structure of microtubule.
Three major classes of antimitotic agents, each with its binding site on
tubulin, act to disrupt tubulin dynamics. Compounds that bind to the taxane
binding
site39
(e.g.,
paclitaxel
and
epothilone)
act
by
preventing
the
depolymerization of tubulin, thus stabilizing microtubules. Compounds that bind to
the vinca alkaloid domain (e.g., vincristine, dolastatins, and cryptophycins) and
colchicine
site
binders
(e.g.,
colchicine
and
combretastatins)
inhibit
the
polymerization of tubulin.39 A number of natural, semi synthetic or fully synthetic
new tubulin inhibitors are currently in clinical development like azaepothilone in
advanced phase III clinical studies.40 Epothilones are more potent microtubule
stabilizers than the taxanes, they are effective against cancer cell lines with high
levels of drug resistance, and they induce the regression of taxane-resistant human
tumors. Epothilone B (patupilone) has been presently being evaluated in phase III
clinical trial. Ixabepilone (Fig. 11), a semi-synthetic analogue of epothilone B, has
recently been granted US FDA approval for the treatment of chemotherapy-resistant
advanced breast cancer.41,42
20
Chapter I
Figure 11. Tubulin target chemotherapeutic agents.
Other classes of compounds which exhibit anticancer activity through the
inhibition of tubulin polymerization are podophyllotoxin,43 and nocodazole.44
Combretastatin A-4 (CA4) (Fig. 12), which is naturally occurring compound was
found to be extremely active inhibitor of tubulin polymerization.45 The major
problem associated with CA4 is poor bioavailability and low aqueous solubility.46
However its disodium phosphate prodrug was developed and is currently in phase
II clinical trails against solid tumours.47,48
Figure 12. Tubulin interacting agents.
21
Chapter I
Since, sulfonamides have been clinically used for many years and found to
posses a large number of biological activities, including antibacterial, anticancer,
diuretic, and antithyroid activities.49 Recently, sulfonamides have been used in
retroviral therapy as HIV protease inhibitors.50 A structure-activity relationship
(SAR) study identified two classes of antitumour sulfonamides, represented by N(3-chloro-7-indolyl)-1,4-benzenedisulfonamide
(E7070)
N-[2-[(4-hydroxy-
and
phenyl)amino]-3-pyridinyl]-4-methoxybenzene sulfonamide (E7010). E7070 and its
analogues belong to a novel class of cell cycle inhibitors that inhibit cell cycle
progression at multiple checkpoints. These compounds exert antitumour properties
by targeting the G1/S and/or G2/M phases of the cell cycle.51 Recently, E7010 (Fig.
13) has been shown to block cells at mitosis by inhibiting tubulin polymerization.
E7010 reversibly binds to the colchicine-binding site of -tubulin, and it displays
antitumour activity against both rodent tumors and several types of human tumor
xenografts.52
N
O O
S
N
H
NH
OCH 3
H2 NO 2S
O O
S
N
H
HN
Cl
OH
E7070
E7010
Figure 13. Tubulin polymerization inhibitors.
BENZOTHIADIAZINES
Benzothiadiazine derivatives (Fig. 14) have shown strong activity against
several cancer cell line with ED50 up to 1.1 g/mL.53 Furthermore, Chern and coworkers have reported fused 1,2,4-benzothiadiazine 1,1-dioxides as potential 1adrenoreceptor antagonists as well as anticancer agents54 and styrylbenzo
thiadiazine
have
exhibited
antitumour
polymerization.55
22
activity
by
inhibiting
tubulin
Chapter I
H 3 CO
O
S
O
O
N
N
N
OH
S
O
O
N
N
N
H
N
N
N
O
S
N
N
H
Figure 14. Anticancer tricyclic benzothiadiazine derivatives.
In addition to this, 1,2,4-benzothiadiazine ring system has shown various
biological activities, for example, chlorothiazide and hydrochlorothiazide (Fig. 15)
exhibits high degree of diuretic activity with lower toxicity.56 However, 7-chloro-3methyl-4H-1,2,4-benzothiadiazine 1,1-dioxide (diazoxide), is one of the most potent
antihypertensive compound which is devoid of the diuretic action.57
O
H 2NO2S
Cl
S
O
N
O
H2NO2S
Cl
N
H
Chlorothiazide
S
O
NH
O
Cl
N
H
S
O
N
N
H
CH3
Diazoxide
Hydrochlorothiazide
Figure 15. Diuretic benzothiadiazines.
Cyclothiazide (Fig. 16) has been found to be one of the most potent
compounds in vitro that by removal of AMPA receptors desensitization enhances
synaptic transmission, but it does not cross the blood-brain barrier. Later, IDRA 21
fulfills this requirement, by inducing cognitive impairments in patas monkey in
improving cognition in rats, and in promoting the induction of long-term
potentiation.58 Furthermore, this class of compounds have recently been shown to
inhibit hepatitis C virus RNA-dependent RNA polymerase.59
H 2NO2S
Cl
O
S
O
NH
Cl
O
OH
NH
N
H
N
H
Cyclothiazide
S
O
O
IDRA-21
O
N
H
CH3
N
O
R
Anti-viral
Figure 16. Bioactive benzothiadiazines.
23
N
S
R = alkyl
Chapter I
CURRENT AREA OF WORK
As discussed above, the design and synthesis of agents capable of specifically
inhibiting the expression of particular proteins critical for tumour cell proliferation,
metastasis or drug resistance is an important. In recent years, combination
chemotherapy with different mechanisms of action is one of the methods that is
being adopted to treat cancer. Therefore, a single molecule containing more than
one pharmacophore, each with different mode of action, could be beneficial for the
treatment of cancer.
PYRROLO[2,1-C][1,4]BENZODIAZEPINES AS DNA BINDING ANTITUMOUR ANTIBIOTICS
10
9
8
N 11
A
7 6
B
5
O
H
11a
N C
3
R8
1
2
CH3O
HO
H
N
R
H3C
H3CHN
Tomaymycin (R7 = OCH3, R8 = OH, R = CH3)
Prothracarcin (R7 = R8 = H, R = CH3)
Sibanomycine (R8 = H, R7 = sibirosamine
pyronoside as in , R = Et)
H
N
OCH3
H
CH3
O
OH OH
Sibiromycin
8
Chicamycin A
OH
N
N
H
N
H3CO
OH
O
H
N
O
CH3
O
HO
H
N
H3CO
R1
CON
R2
Anthramycin (R8 = CH3, R9 = R1 = R2 = H)
Mazethramycin (R8 = R1 = CH3, R9 = R2 = H)
Porothramycin B (R8 = H, R9 = R1 = R2 = CH3)
O
HO
H
O
N
R7
OCH3
N
PBD ring system
R8
OR9 H
N
O
R1 R2
Neothramycin A ( R1 = H; R2 = OH)
Neothramycin B ( R1 = OH, R2 = H)
DC-81 (R1 = R2 = H)
Figure 17. Naturally occurring PBDs.
24
Chapter I
The pyrrolo[2,1-c][1,4]benzodiazepines (PBDs) are a family of DNAinteractive antitumour antibiotics derived from various Streptomyces species. To
date
thirteen
structures
which
include
anthramycin,60
mezethramycin,61
porothramycin,62 prothracarcin,63 sibanomycine,64 tomaymycin,65 sibiromycin,66
chicamycin A,67 neothramycin A, B68 DC-81,69 and abbeymycin70 have been isolated
from various Streptomyces species (Fig. 17).
PBD-DNA INTERACTIONS
The known PBD natural products have a (S)-configuration at the C11aposition, which provides them with a right-handed twist when viewed from the Cring towards the A-ring. This has given the appropriate three-dimensional shape for
isohelicity with the minor groove of DNA, leading to a snug fit at the binding site.
Recemization at C11a can significantly reduce both DNA binding affinity and in
vitro cytotoxicity. A synthetic PBD with the (R)-configuration at C11a was shown to
be devoid of both DNA binding affinity and in vitro cytotoxicity. The N10-C11 imine
moiety may exist in the hydrated form depending upon precise structure of the
compound and the method of isolation or synthetic work up. Imines and methyl
ether forms are interconvertable by dissolution of imine in methanol or by several
cycles of refluxing the methyl ether in chloroform followed by evaporation of the
solvent in vacuum. 71
N
H
H2 O
N
O
H
N
N
-H 2O
O
CH 3OH
-CH 3OH
OH
H
H
N
OCH 3
H
N
O
25
H 2O
CH 3OH
Chapter I
The pyrrolo[2,1-c][1,4]benzodiazepine (PBD) interactions with DNA are
unique since they bind within the minor groove of DNA forming a covalent aminal
bond between the C11-position of the central B-ring and the N2 amino group of a
guanine base.72 The cytotoxic and antitumour activity of PBDs are attributed to their
ability to form covalent DNA adducts. Molecular modeling, solution NMR,
fluorimetry and DNA foot printing experiments have shown that these molecules
have a preferred selectivity for Pu-G-Pu sequences73 are oriented with their A-rings
pointed either towards the 3' or 5' end of the covalently bonded DNA strand (as in
case of anthramycin and tomaymycin). The PBDs have been shown to interfere with
the action of endonuclease enzymes on DNA and to block transcription by
inhibiting DNA polymerase in a sequence specific manner74 processes which may
be relevant for the biological activity.
NH2-Guanine-DNA
H
N
OR
H
R =H
R = CH3
N
O
NH2
N
Guanine-DNA
H
N
N
O
NH-Guanine-DNA
H
NH2-Guanine-DNA
N
N
H
N
O
O
26
Chapter I
STRUCTURE-ACTIVITY RELATIONSHIPS
Structure activity relationships (SAR) for this ring system have been derived
by Thurston and co-workers as shown below.
(g) Electron-donating
substituents required
at position 7,8 or 9
of A-ring
(h) Bulky substituents at N10
(eg. acetyl) inhibit DNAbinding and cytotoxicity
(b) (S)-Stereochemistry
required at C11a
R9
R8
R7
(f ) Sugar moiety at C7
enhances DNA-binding
af f inity and cytotoxicity
in some cell lines
(a) An imine, carbinolamine
methyl ether required at N10-C11
N
10
11
N
H
11a
O
3
1
2
(c) Replacement of C1 with
an oxygen maintains
cytotoxicity
R
(d) Endocyclic or exocyclic
unsaturation at C2 enhances
cytotoxicity and in vivo
antitumour activity. Fully
unsaturated C-ring leads to
(e) Small substituents (eg. -OH) complete loss of DNA-binding
tolerated at C3 in f ully saturated and cytotoxicity
C-ring compounds
SYNTHETIC APPROACHES FOR PYRROLO[2,1-C][1,4]BENZODIAZEPINES
The first total synthesis of a carbinolamine containing PBD of anthramycin
has been reported by Leimgruber in 1968.6475 Extensive reviews of the synthetic
literature of the PBDs have appeared in 1994, 1998 and 2002.76 Various approaches
to the synthesis of PBD antibiotics have been investigated, including hydride
reduction of seven member cyclic dilactams,77 reductive cyclization of acyclic
nitroaldehydes,78 iminothioether approach79 cyclization of aminothioacetals,80
deprotective cyclization of the diethylthioacetals via N10 protected precursors,81
oxidation of cyclic secondary amines,82 reductive cyclizations83 and solid phase
approaches. 84
27
Chapter I
KANEKO APPROACH (IMINOTHIOETHER REDUCTION)
Kaneko and co-workers77a have developed an efficient method for the
reduction of PBD dilactams to the carbinolamine using aluminium amalgam. This
methodology has been extended to the preparation of bicyclic and tricyclic
analogues of anthramycin, the total synthesis of some naturally occurring PBDs like
chicamycin.79b By using this approach Baraldi and co-workers have synthesized
some heterocyclic PBD analogues in which the A ring of PBD skeleton is replaced
with a 1,3 or 1,5-disubstituted pyrazole nucleus.
H
N
R1
R1
R2
H
N
R2
O
H
N
O
(i)
R2
N
R1
R2
N
O
R3
O
R2
(v)
S
R1
R2
SR 4
H
N
N
R3
O
H
N
R3
S
(iii)
N
H
N
R3
O
(iv)
+
R3
(ii)
R1
R2
H
N
R1
OCH 3
H
H
+
R3
R1
H
N
S
R1
R2
H
N
H
N
O
H
N
SR 4
H
N
O
R3
R3
R 1 = H, OH, OBn, OCH3 , OAc
R 2 = H, OCH3
R 3 = H, = CH-CH 3 (E), OH (a), OAc (b), = CH-COOEt (E)
R 4 = CH 3
Reagents and condit ions: (i) P 2S 5, C6 H 6, 80 o C or P2 S 5, NaHCO3 , CH3 CN, 15 min, or (pCH3 OC 6H 4PS 2 )2 , C 6H 6, 80 o C; (ii) Et 3 OBF4 , CH 2 Cl2 , KHCO3 or CH3 I, K 2CO3 , THF or DMF; (iii) AlHg, aq.THF or KH 2PO4 , 0-5 oC, 14 h; (iv) 0.1 N methanolic HgCl2 , 0 oC or SiO2 chromatography,
5 o C; (v) CH 3 OH.
28
Chapter I
THURSTON’S APPROACH
Thurston and co-workers70a have developed an efficient method for the
synthesis of various PBDs containing carbinolamine moiety by employing mercuric
chloride (HgCl2) and calcium carbonate (CaCO3) in aqueous acetonitrile at room
temperature.
RO
H 3CO
PhH2 CO
(ii)
NO2
H3 CO
COOH
(iii)
COOH
PhH 2 CO
NO2 CH(SEt)
2
N
H 3 CO
O
(i)
aR=H
b R = PhCH 2
(iv)
RO
N
H
(v)
N
H 3CO
O
(vi)
PhH 2CO
NH 2
H 3CO
N
CH(SEt)2
O
a R = PhCH 2
b R=H
Reagents and conditions : (i) PhCH 2Cl, THF, NaOH, H2 O, reflux, 48 h; (ii) SnCl4, HNO 3, CH 2 Cl2 , 25 o C,5 min; (iii) (COCl) 2, THF, DMF, 3 h then, pyrrolidine-2-carboxaldehyde diethyl thioacetal,
Et3 N, H2 O, 0 oC, 1.5 h; (iv) SnCl2.2H2 O, MeOH, reflux, 45 min; (v) HgCl2 , CaCO3 , CH3 CN-H 2 O, 12
h; (vi) 10% Pd-C, EtOH, cyclohexadiene, 3 h.
Baraldi and co-workers85 synthesized hybrid molecules containing PBD and
minor groove binding oligo-pyrrole carriers, while Hurley and co-workers86 have
synthesized AT-groove binding hybrids by using this approach. In the same manner
Suzuki coupling of C7 aryl substituted PBDs have been synthesized by Thurston
and co-workers.87 This B-ring strategy of Fukuyama and coworkers has also been
employed for the synthesis of C2/C2'-exo-unsaturated PBD dimer, C2-C3/C2'-C3'endo unsaturated PBD dimer with remarkable covalent DNA binding affinity.
29
Chapter I
C8-LINKED PYRROLO[2,1-C][1,4]BENZODIAZEPINE HYBRIDS
In the search for compounds with better antitumour selectivity and DNA
sequence specificity many C8-linked hybrids of pyrrolo[2,1-c][1,4]benzodiazepines
have been prepared. In recent years, bifunctional DNA interactive agents
comprising of two types of antitumour agents joined by a linker have attracted
considerable attention as a new class of antitumour agents. These compounds are
capable of recognizing heterogeneous DNA sequences.
Baraldi and co-workers88 have been designed and synthesized distamycinPBD and netropsin-PBD conjugates as novel sequence selective C8-linked PBD
hybrids. These hybrids containing 1 to 4 pyrrole units have been investigated for the
sequence selectivity and stability of DNA drug complexes.
H 2N
H
N
H
N
HCl HN
O
N
N
O
O
n
H
N
H3 CO
O
n = 1-4
Hurley and co-workers89 have synthesized novel DNA-DNA interstrand
adenine-guanine cross-linking UTA-6026 compound. Preliminary in vitro tests
showed that UTA-6026 has remarkably potent cytotoxicity to several tumour cell
lines (IC50 = 0.28 nM in human breast tumour cell line MCF-7, IC50 = 0.047 nM in
colon tumour cell line SW-480 and IC50 = 5.1 nM in human lung tumour cell line
A549).
H 3C
N
H
H
N
N
O
O
N
O
N
H
N
H3CO
O
H
O
Lown and co-workers90 have also reported the synthesis of a series of PBDlexitropsin conjugates linked through the C8 position with a suitable linker. The
conjugation has been achieved by amidic linkage to amine of the lexitropsin unit
30
Chapter I
with the acid moiety of the linker attached to the PBD system. These compounds
have been synthesized in view of the effect with sequence selective binding in DNA
duplex.
H
N
CH3
H 3C
H
N
N
H
O
N
O
O
N
H3 CO
n
H
O
n = 1-3
Denny and co-workers91 have designed and synthesized unsymmetrical
DNA cross-linkers by linking the seco-1,2,9,9a-tetrahydrocyclopropa[c]benz[e]indo4-one (seco-CBI) to PBD moiety. These compounds have anticipated cross-linking
between N3 of adenine and N2 of guanine in the minor groove of DNA.
Cl
O
N
O
N
H
N
H3CO
O
OH
Thurston and co-workers92 have been reported the synthesis and anticancer
activity of C8-epoxide linked pyrrolo[2,1-c][1,4]benzodiazepine.
O
N
O
H
N
H3CO
O
Recently, Wang and co-workers93 have designed and synthesized novel PBDindole conjugates. Further, these conjugates have been tested against a panel of 60
human cancer cell lines by NCI and demonstrated that PBD-indole conjugates
exhibited a higher level of cytotoxic activity than the existing natural and synthetic
PBDs and can activate the apoptotic pathway mediated by mitochondria.
31
Chapter I
N
O
N
H
O
H3 CO
H
N
O
Lown and co-workers94 have designed and synthesized novel PBDgylcosylated pyrrol and imidazole polyamide conjugates and described as water
insoluble and water-soluble PBD conjugates.
H OH
HO
N
H
N
H
HO
H
OH
O
O
OCH 3
O
H
OH
N
N
H
N
H
n = 1, 2
H OH
HO
N
H
N
OCH3
O
H
H
OH
CH3 O
N
O
O
O
X
NH
n
N
CH 3
CH 3
HO
OH
N
N
H
H
O
N
H
n
N
CH 3
CH 3
X = CH, n = 2
X = N, n = 2
Kamal and co-workers95 have synthesized a series of PBD conjugates by
linking different DNA interacting ligands such as benzimidazole, polyaromatic
hydrocarbons (pyrene amine and chrysene amine), anthraquinones, by using
varying linker length to enhance the DNA binding affinity and antitumour activity.
All these prepared molecules have shown good DNA binding affinity with better
anticancer activity.
32
Chapter I
H
N
N
H 3C
O
N
N
(CH 2) n O
N
N
H3 CO
O
n = 3-5
O
H
N
(CH2 )n O
N
O
H 3CO
O
H
HN
n
O
H 3CO
N
O
n = 3-4
H
O
N
H
N
O
n = 3-4
Kamal and co-workers96 have designed and synthesized PBD-morpholine, N-methyl
piperizine and N,N-dimethyl amine hybrids in attempts to improve the water
solubility and cytotoxicity of the PBD compounds.
O
N
O
N
H
N
H 3CO
O
APOPTOSIS AS CELLULAR TARGET FOR CANCER
Apoptosis, is a physiological process that plays a essential role in controlling cell
number in many developmental and physiological settings and in chemotherapyinduced tumour-cell killing.97-100 It is a genetically regulated biological process,
guided by the ratio of proapoptotic and antiapoptotic proteins.101 Inhibition of
apoptosis enhances the survival of cancer cells and facilitates their escape from
immune surveillance and cytotoxic therapies. Among the principal molecules
contributing to this phenomenon are the inhibitor of apoptosis (IAP) proteins, a
family of anti apoptotic regulators that block cell death in response to diverse stimuli
through interactions with inducers and effectors of apoptosis.102
There are two major apoptosis signaling pathways, that is, the death receptor
(extrinsic) pathway and the mitichondria (intrinsic) pathway (Fig. 18)103 Apoptosis is
executed by a subfamily of cysteine proteases known as caspases under most
circumstances, activation of either pathway eventually leads to proteolytic cleavage
33
Chapter I
and thus activation of caspases, that act as common death effector molecules.
Caspases are responsible for many of the biochemical and morphological hallmarks of
apoptotic ell death by cleaving a range of substrates in cytoplasm or nucleus.104 In
mammalian cells, a major caspase activation pathway is the cytochrome c-initiated
pathway. In this pathway, a variety of apoptotic stimuli cause cytochrome c release
from mitochondria, which in turn induces a series of biochemical reactions that result
in caspase activation and subsequent cell death.104 Disruption of mitochondrial
fuction appears to be an early feature of apoptotic cell death. Several different
biochemical changes have been shown, including the generation of reactive oxygen
species (ROS), calcium flux, loss of the mitochondrial membrane potential, and
cytochrome release.105 The mitochondrial pathway of apoptosis proceeds when
molecules sequestered between the outer and inner mitochondrial membranes are
released to the cytosol by mitochondrial outer membrane permeabilization (MOMP).
This process is controlled by the BCL-2 family, which is composed of both pro- and
anti-apoptotic proteins.106 Apoptosis is also highly characterized by a series of typical
morphological events, such as DNA fragmentation, chromatin condensation,
membrane blebbing and cell shrinkage. Cells undergoing apoptosis ultimately
dissameble into membrane enclosed vesicles (apoptotic bodies) that are engulfied by
neighbouring cells and phagocytes, thus preventing an inflammatory response.107
34
Chapter I
Figure 18. Schematic representation of apoptosis pathway.
Further, killing of cancer cells by current therapies is largely due to induction
of apoptosis in tumour cells. Since a hallmark of human cancers is their resistance to
apoptosis, there is a demand to develop novel strategies that restore the apoptotic
machinery in order to overcome cancer resistance.108 Numerous novel approaches are
currently being followed employing gene therapy and antisense strategies,
recombinant biologics or classical organic and combinatorial chemistry in order to
target specific apoptotic regulators.109-112 New drugs that could modulate the
expression of molecules involved in the apoptotic pathway with the ability to induce
apoptosis in multidrug-resistant or apoptosis resistant tumour cell lines are of great
importance in cancer chemotherapy. Therefore the identification of apoptosis
inducers represents an attractive approach for the discovery and develpomemt of
potential anticancer agents.Moreover, by induceing apoptosis, these new agents may
overcome tumour resitance to conventional anticancer agents.113
35
Chapter I
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