Question 1

a. Briefly discuss the evolution of drug discovery of anti-neoplastic

agents. Your discussion should include at least 3 examples of drugs and
technologies.

The evolution of drug discovery for anti-neoplastic agents has come a long way and is
marked by significant breakthroughs that have revolutionized cancer treatment.
The discovery of chemotherapy in the 1940s marked the first significant step. The
first anti-neoplastic agent, Nitrogen Mustard, was discovered during World War II
when soldiers exposed to mustard gas were found to have low white blood cell
counts, suggesting a possible mechanism for cancer treatment. This led to the
development of alkylating agents, a class of drugs that work by attaching an alkyl
group to the DNA of cancer cells, disrupting their growth and reproduction.
In the 1960s, the development of Cytarabine, a pyrimidine analog, marked the
advancement of antimetabolites as anti-cancer drugs. These drugs work by mimicking
the cellular substances needed for DNA synthesis, thereby inhibiting the growth and
replication of cancer cells. Cytarabine has been vastly used for the treatment of acute
myeloid leukemia.
The late 20th century saw the rise of targeted therapies, an advancement that allowed
for more precise treatments with fewer side effects. One remarkable example is the
development of Imatinib (Gleevec) in the late 1990s. As a tyrosine-kinase inhibitor, it
targets specific proteins involved in the growth and development of cancer cells. This
drug marked a new era in cancer treatment, as it effectively transformed chronic
myeloid leukemia from a fatal disease into a manageable condition.
Technological advancements have also played a significant role in the evolution of
anti-neoplastic drug discovery. High throughput screening (HTS) technologies have
enabled rapid testing of thousands of compounds, speeding up the drug discovery
process. Additionally, the advent of computational models and bioinformatics has
facilitated the understanding of cancer at a molecular level, leading to the
development of more targeted therapies.
In recent years, the rise of immunotherapies, such as the checkpoint inhibitor
Pembrolizumab, has opened up a new frontier in cancer treatment. These drugs work
by harnessing the body's immune system to fight cancer, offering a new approach to
anti-neoplastic therapy.

Using the structure of mechlorethamine hydrochloride and guanine, illustrate the mechanism of
DNA alkylation by nitrogen mustards.

In the mechanism of DNA alkylation by nitrogen mustards like mechlorethamine hydrochloride,

the process involves the formation of an electrophilic alkylating agent that reacts with DNA,
leading to the formation of covalent DNA adducts. Guanine, one of the nucleobases in DNA, is a
common target for alkylation by nitrogen mustards. Here's an overview of the mechanism:
**1. Structure of Mechlorethamine Hydrochloride**:
- **Chemical Formula**: C5H11Cl2N
- **Structure**:
- N(CH2CH2Cl)2 (Mechlorethamine)
- Cl- (Chloride ion)

**2. Structure of Guanine**:

- Guanine is one of the four nucleobases found in DNA.
- **Chemical Formula**: C5H5N5O

**3. Mechanism of DNA Alkylation**:

**Step 1: Activation of Mechlorethamine**:

- Mechlorethamine hydrochloride undergoes chemical activation, often through metabolic
processes, to form reactive alkylating species. This can include the release of reactive
intermediates like aziridinium ions.

**Step 2: Nucleophilic Attack**:

- The activated mechlorethamine molecule acts as an electrophile due to the presence of the
alkyl group.
- Guanine within the DNA molecule, being a nucleophile (due to its lone pair of electrons on
nitrogen), undergoes nucleophilic attack on the electrophilic carbon of the alkylating agent.

**Step 3: Covalent Bond Formation**:

- A covalent bond is formed between the N7 position of guanine and the alkyl group from
mechlorethamine.
- This covalent bond alters the structure of the DNA molecule, leading to the formation of a bulky
DNA adduct.

**Step 4: Impact on DNA Function**:

- The covalent modification of guanine by the alkyl group can disrupt normal DNA structure and
function.
- The bulky adduct can interfere with DNA replication and transcription processes, leading to
mutations or DNA strand breaks.

**Step 5: Biological Consequences**:

- Alkylation of guanine in DNA can trigger cellular responses, including DNA repair mechanisms.
- Unrepaired or misrepaired DNA lesions caused by alkylation can result in cell death or
contribute to carcinogenesis.

In conclusion, the mechanism of DNA alkylation by nitrogen mustards like mechlorethamine

hydrochloride involves the formation of reactive alkylating species that covalently modify DNA
bases such as guanine, leading to altered DNA structure, genetic mutations, and potential
cytotoxic effects on cells.

bi) What are 2 potential effects of DNA alkylation?

Two potential effects of DNA alkylation are:

1. **DNA Damage and Mutagenesis**:

- DNA alkylation can lead to the formation of covalent adducts between the alkyl group and
DNA bases, such as guanine.
- These adducts can cause structural distortions in DNA, leading to errors during DNA
replication or transcription.
- Mutations resulting from DNA alkylation can disrupt normal cellular processes, potentially
contributing to the development of cancer or other genetic diseases.

2. **Induction of Cell Death**:

- Severe DNA alkylation can trigger cell death pathways, such as apoptosis or necrosis.
- Cells with extensively damaged DNA may undergo programmed cell death to prevent the
propagation of genetic abnormalities.
- The induction of cell death by DNA alkylation is a mechanism employed in cancer therapy to
target rapidly dividing cancer cells.

bii) Name an analogue of mechlorethamine, and explain how it improves on the prototypical
molecule? [3]
An analogue of mechlorethamine is **Cyclophosphamide**, which is a nitrogen mustard
alkylating agent commonly used in chemotherapy.

**Improvements of Cyclophosphamide over Mechlorethamine**:

1. **Increased Selectivity**:
- Cyclophosphamide is a prodrug that requires metabolic activation in the liver to form its active
alkylating metabolite. This activation step imparts selectivity to the drug, as the conversion
mainly occurs in tumor tissues due to higher levels of specific liver enzymes.
- This selective activation reduces the systemic toxicity associated with mechlorethamine,
allowing for higher doses to be administered to cancer cells while sparing normal tissues.

2. **Enhanced Pharmacokinetics**:
- Cyclophosphamide exhibits improved pharmacokinetic properties compared to
mechlorethamine. It has better oral bioavailability, allowing for convenient administration in pill
form.
- The prodrug nature of cyclophosphamide also provides a longer half-life compared to
mechlorethamine, leading to sustained exposure to the active metabolite.

3. **Broader Spectrum of Activity**:

 - Cyclophosphamide demonstrates a broader spectrum of antitumor activity compared to
mechlorethamine. It is effective against various types of cancers, including lymphomas,
leukemias, and solid tumors.
- The versatility of cyclophosphamide in treating different cancer types has made it a
cornerstone in combination chemotherapy regimens.

c. i) What is the function of ribonucleotide reductase, and which vital element is required to
initiate the catalytic cycle? [2]

The function of **ribonucleotide reductase** is to catalyze the conversion of ribonucleotides

(RNA building blocks) to deoxyribonucleotides (DNA building blocks) through a reduction
reaction, which is an essential step in DNA synthesis and repair.

To initiate the catalytic cycle, ribonucleotide reductase requires the presence of the vital element
**iron** (Fe). Iron plays a crucial role in the active site of ribonucleotide reductase, where it
facilitates the reduction of ribonucleotides to deoxyribonucleotides by donating electrons during
the enzymatic reaction.

ii) Using the chemical structure illustrate the mechanism by which hydroxyurea stops the catalytic
cycle. [2]

Hydroxyurea is a potent inhibitor of ribonucleotide reductase, disrupting the enzymatic activity

essential for DNA synthesis. The mechanism by which hydroxyurea stops the catalytic cycle of
ribonucleotide reductase involves the formation of a covalent bond with the active site iron
center. This interaction leads to the inactivation of the enzyme and hinders the conversion of
ribonucleotides to deoxyribonucleotides.

Here is a simplified representation of the mechanism using the chemical structures:

- The active form of ribonucleotide reductase includes an iron center (Fe) surrounded by a tyrosyl
radical that participates in the reduction reaction.
- Hydroxyurea (represented as HU) forms a covalent bond with the iron center, preventing the
tyrosyl radical from engaging in the reduction of ribonucleotides.
- This disruption halts the catalytic cycle of ribonucleotide reductase, inhibiting the production of
deoxyribonucleotides and ultimately interfering with DNA synthesis.

By interfering with the enzymatic activity of ribonucleotide reductase, hydroxyurea serves as a

valuable tool in cancer therapy and other medical contexts where inhibition of DNA synthesis is
desired.

iii) Which position on pyrimidine analogues is modified in order to inhibit of ribonucleotide

reductase? [1]
The position on **pyrimidine analogues** that is typically modified to inhibit ribonucleotide
reductase is the **C2 position**. This modification is crucial for the analogues to effectively
interfere with the catalytic activity of ribonucleotide reductase, disrupting the conversion of
ribonucleotides to deoxyribonucleotides and hindering DNA synthesis.

d. The structure of imatinib is provided below. Using the chemical structure as well as a narrative
to illustrate structure activity relationships of the molecule with tyrosine kinase enzyme. [10]

Imatinib is a potent tyrosine kinase inhibitor used in the treatment of cancers such as chronic
myeloid leukemia (CML) and gastrointestinal stromal tumors (GIST). Its structure consists of a
**bis-aryl urea** backbone with several key functional groups that contribute to its activity
against tyrosine kinases.

The structure-activity relationship (SAR) of imatinib with tyrosine kinase enzymes can be
elucidated as follows:

1. **Bis-aryl Urea Backbone**:

- The bis-aryl urea backbone is essential for the inhibitory activity of imatinib. It serves as the
scaffold that positions the functional groups for interactions with the enzyme.

2. **3-Phenylaminopyridine Moiety**:
- The 3-phenylaminopyridine moiety in imatinib plays a crucial role in binding to the ATP-
binding pocket of tyrosine kinases. This interaction is vital for blocking the ATP binding site and
inhibiting kinase activity.

3. **Methylpiperazine Ring**:
- The presence of the methylpiperazine ring enhances the solubility and bioavailability of
imatinib. It also contributes to interactions with the enzyme through hydrogen bonding.

4. **N-Methylpiperazine Terminal Group**:

- The N-methylpiperazine terminal group aids in the binding of imatinib to the allosteric site of
the kinase, promoting selectivity and inhibitory potency.

5. **4-Methylpiperazine Group**:
- The 4-methylpiperazine group contributes to the overall pharmacokinetic properties of
imatinib, influencing its distribution and metabolism in the body.

a. What are antimetabolites? Classify the chemotherapeutic agents acting as antimetabolites

with examples (8)
Antimetabolites are a class of chemotherapeutic agents that interfere with the normal metabolic
processes of cells by acting as structural analogs of essential cellular components. These agents
disrupt DNA and RNA synthesis, as well as other critical cellular functions, ultimately leading to
cell death. Antimetabolites are commonly used in cancer treatment to inhibit the growth of
rapidly dividing cancer cells.

**Classification of Chemotherapeutic Agents Acting as Antimetabolites with Examples**:

1. **Pyrimidine Analog Antimetabolites**:

- These compounds mimic the structure of pyrimidine nucleotides, interfering with DNA and
RNA synthesis.
- *Examples*:
- 5-Fluorouracil (5-FU): Inhibits thymidylate synthase, disrupting DNA synthesis.
- Cytarabine (ARA-C): Incorporates into DNA, leading to chain termination.

2. **Purine Analog Antimetabolites**:

- These agents resemble purine nucleotides, affecting DNA and RNA synthesis.
- *Examples*:
- 6-Mercaptopurine (6-MP): Inhibits purine synthesis and disrupts DNA replication.
- Fludarabine: Inhibits DNA synthesis and repair processes in cells.

3. **Folate Antagonists**:
- These antimetabolites interfere with folate metabolism, crucial for nucleotide synthesis.
- *Examples*:
- Methotrexate: Inhibits dihydrofolate reductase, reducing available folate for DNA synthesis.
- Pemetrexed: Inhibits multiple folate-dependent enzymes, impeding DNA and RNA synthesis.

4. **Antifolate Antimetabolites**:
- These agents block folic acid metabolism, essential for nucleotide synthesis.
- *Examples*:
- Raltitrexed: Inhibits thymidylate synthase, hindering thymidine synthesis.
- Pralatrexate: Blocks dihydrofolate reductase, affecting purine and pyrimidine synthesis.

5. **Adenosine Analog Antimetabolites**:

- These compounds resemble adenosine nucleotides, disrupting RNA and protein synthesis.
- *Examples*:
- Cladribine: Incorporates into DNA, leading to inhibition of DNA repair mechanisms.
- Gemcitabine: Inhibits DNA polymerase, impairing DNA synthesis.

Write notes on the following:

i. HIV protease inhibitors (8)
**Detailed Outline Notes on HIV Protease Inhibitors**:

**I. Introduction to HIV Protease Inhibitors**:

- HIV protease inhibitors are a class of antiretroviral drugs used in the treatment of HIV/AIDS.
- These inhibitors target the HIV protease enzyme, crucial for viral replication by cleaving viral
polyproteins into functional proteins necessary for the formation of infectious viral particles.

**II. Mechanism of Action**:

- **Target**: HIV protease enzyme.
- **Inhibition**: Bind to the active site of the protease enzyme, preventing the cleavage of viral
polyproteins.
- **Interference**: Disrupt the maturation of new viral particles, rendering them non-infectious.

**III. Examples of HIV Protease Inhibitors**:

- **First-Generation**:
1. Saquinavir.
2. Ritonavir.
3. Indinavir.
- **Second-Generation (Improved Pharmacokinetics)**:
1. Atazanavir.
2. Darunavir.
3. Lopinavir.
- **Newer Agents**:
1. Fosamprenavir.
2. Tipranavir.
3. Nelfinavir.

**IV. Pharmacokinetics**:
- **Absorption**: Varied oral bioavailability. Some require boosting with ritonavir.
- **Distribution**: Widely distributed in tissues.
- **Metabolism**: Extensively metabolized by the liver (CYP3A4).
- **Excretion**: Primarily renal excretion as metabolites.

**V. Adverse Effects**:

- **Gastrointestinal**: Nausea, diarrhea, abdominal pain.
- **Metabolic**: Lipodystrophy, dyslipidemia, insulin resistance.
- **Drug Interactions**: Potent CYP3A4 inhibitors or inducers.
- **Cardiovascular**: Increased risk of cardiovascular events.
- **Endocrine**: Risk of diabetes mellitus.

**VI. Resistance and Cross-Resistance**:

- **Mechanisms**: Mutations in the protease gene leading to reduced drug binding affinity.
- **Cross-Resistance**: Common mutations resulting in resistance to multiple protease
inhibitors.

**VII. Clinical Use**:

- **Treatment**: Combined with other antiretroviral agents in highly active antiretroviral therapy
(HAART).
- **Prevention**: Used in post-exposure prophylaxis (PEP) and pre-exposure prophylaxis (PrEP)
in high-risk populations.

**VIII. Future Developments**:

- **New Agents**: Continued development of novel protease inhibitors with improved efficacy
and reduced side effects.
- **Combination Therapies**: Integration of protease inhibitors into single-tablet regimens for
enhanced patient adherence.

In conclusion, HIV protease inhibitors play a significant role in the management of HIV/AIDS by
targeting a key enzyme essential for viral replication. Understanding their mechanism of action,
pharmacokinetics, adverse effects, resistance patterns, and clinical applications is crucial for
optimizing treatment outcomes in patients with HIV infection.

ii. Explain how changes in metabolic pathways (e.g., induction, inhibition) can impact the
therapeutic activity, toxicity, and/or drug interactions (9)

**Impact of Changes in Metabolic Pathways on Therapeutic Activity, Toxicity, and Drug

Interactions**:

**I. Introduction**:
Metabolic pathways play a crucial role in determining the fate of drugs within the body. Changes
in these pathways, such as induction or inhibition, can significantly influence the therapeutic
efficacy, toxicity, and potential drug interactions of medications.

**II. Effects of Metabolic Changes**:

1. **Induction of Metabolic Pathways**:

- **Effects**:
- **Enhanced Drug Metabolism**: Increased activity of drug-metabolizing enzymes (e.g.,
cytochrome P450 enzymes) can lead to accelerated drug clearance.
- **Reduced Drug Concentrations**: Faster metabolism can decrease drug levels, reducing
therapeutic efficacy.
- **Potential Therapeutic Failure**: Suboptimal drug concentrations may result in treatment
failure.
- **Risk of Resistance**: Inadequate drug exposure can promote the development of drug
resistance in pathogens or cancer cells.

2. **Inhibition of Metabolic Pathways**:

- **Effects**:
- **Decreased Drug Metabolism**: Inhibition of metabolic enzymes can lead to reduced drug
clearance.
- **Increased Drug Concentrations**: Slower metabolism can cause drug accumulation,
potentially leading to toxicity.
- **Enhanced Therapeutic Effects**: Higher drug concentrations may result in enhanced
therapeutic activity.
- **Risk of Adverse Effects**: Toxicity may occur due to elevated drug levels beyond the
therapeutic range.

**III. Impact on Drug Interactions**:

- **Enzyme Inhibition**:
- **Pharmacokinetic Interactions**: Inhibitors of drug-metabolizing enzymes can alter the
pharmacokinetics of co-administered drugs.
- **Risk of Toxicity**: Accumulation of drugs metabolized by the inhibited enzyme can lead to
toxicity.
- **Enzyme Induction**:
- **Reduced Drug Levels**: Drugs metabolized by induced enzymes may have decreased
concentrations and reduced efficacy.
- **Therapeutic Failure**: Diminished drug exposure due to induction can compromise
treatment outcomes.

**IV. Clinical Implications**:

- Understanding the metabolic changes induced by drugs is crucial for predicting and managing
drug interactions, toxicity, and treatment outcomes.
- Close monitoring of drug levels, therapeutic responses, and potential adverse effects is
essential when metabolic pathways are altered.

**V. Conclusion**:
Changes in metabolic pathways, whether through induction or inhibition, can have profound
effects on the therapeutic activity, toxicity, and drug interactions of medications. Clinicians must
consider these factors when prescribing drugs to ensure optimal treatment outcomes and
minimize the risk of adverse events associated with altered drug metabolism.

Question 3
a. Explain how genetic differences in drug metabolism result in predictable differences in drug
response (5)
b. Describe the differences in the ways that bacteria and viruses multiply (3)

a. Genetic differences in drug metabolism can lead to variations in drug response due to the role
that enzymes play in metabolizing drugs in the body. Enzymes are proteins encoded by genes,
and variations in these genes can affect the activity of the enzymes involved in drug metabolism.
For instance, some people may have genetic variants that result in lower levels of an enzyme
responsible for metabolizing a specific drug, leading to slower drug clearance from the body. This
can result in higher drug concentrations in the blood, potentially causing toxicity or adverse
effects. On the other hand, individuals with genetic variations that enhance the activity of drug-
metabolizing enzymes may metabolize drugs more rapidly, leading to lower drug levels and
reduced efficacy. Understanding these genetic differences can help predict how individuals will
respond to certain drugs, allowing for personalized medicine approaches that optimize treatment
outcomes and minimize adverse reactions.

b. Bacteria and viruses have distinct mechanisms of multiplication. Bacteria reproduce asexually
through binary fission, where a single bacterial cell divides into two identical daughter cells. This
process results in exponential growth of bacterial populations under favorable conditions. In
contrast, viruses require a host cell to replicate. They invade host cells and hijack the cell's
machinery to produce multiple copies of the virus. This process often leads to the destruction of
the host cell. The replication of viruses involves steps such as attachment to the host cell, entry,
replication of viral genetic material, assembly of new viruses, and release from the host cell.
Unlike bacteria, viruses cannot reproduce independently and rely on host cells to multiply.

c. The effect of some drugs used to treat cancer depends on geometrical isomerism. One
successful anti-cancer drug is cisplatin, whose formula is PtCl2 (NH3)2. Describe the structure of
cisplatin by referring to the following:
i. The meaning of the term geometrical isomerism as applied to cisplatin
ii. Diagrams to show the structure of cisplatin and its geometrical isomer
iii. The types of bonding in cisplatin. (6)

i. **The Meaning of Geometrical Isomerism as Applied to Cisplatin**:

Geometrical isomerism, also known as cis-trans isomerism, is a type of stereoisomerism where

the spatial arrangement of atoms or groups around a double bond, in a ring, or in a coordination
compound is important. In the case of cisplatin, geometrical isomerism arises due to the
arrangement of ligands around the central platinum atom. In cisplatin, the chloride ions and
ammonia molecules are arranged on the same side compared to transplatin, where these ligands
are on opposite sides. This difference in spatial arrangement results in different geometrical
isomers with distinct properties.

ii. **Diagrams Showing the Structure of Cisplatin and Its Geometrical Isomer**:

- **Structure of Cisplatin (cis Configuration)**:

Cl NH3
\ /
Pt
/ \
NH3 Cl

- **Structure of Transplatin (trans Configuration)**:

 Cl Cl
\ /
Pt
/ \
NH3 NH3

iii. **Types of Bonding in Cisplatin**:

- **Coordinate Covalent Bonds**: The bonding in cisplatin involves coordinate covalent bonds.
The ligands (chloride ions and ammonia molecules) donate electron pairs to the platinum atom,
forming these coordinate covalent bonds. The platinum atom acts as the Lewis acid, accepting
electron pairs from the Lewis bases (ligands) to form stable complexes.

In summary, cisplatin exhibits geometrical isomerism due to the arrangement of its ligands
around the central platinum atom. The two possible geometric isomers, cisplatin and transplatin,
have distinct spatial arrangements of the ligands. The bonding in cisplatin involves coordinate
covalent bonds, where the ligands provide electron pairs to the central platinum atom, forming
stable coordination complexes.

d. Explain the catalytic mechanism of CYP450 enzyme (11)

The catalytic mechanism of the Cytochrome P450 (CYP450) enzyme involves several steps that
are crucial for its function as a monooxygenase enzyme. Here is a detailed explanation of the
catalytic mechanism of the CYP450 enzyme:

1. **Substrate Binding**:
- The substrate, typically a hydrophobic molecule like a drug or xenobiotic, enters the active site
of the CYP450 enzyme.
- The active site of CYP450 contains a heme cofactor with an iron atom at its center. This iron
atom can form complexes with oxygen molecules.

2. **Reduction of CYP450**:
- NADPH-cytochrome P450 reductase transfers two electrons from NADPH to the CYP450
enzyme.
- This reduction step converts the iron atom in the heme group from Fe3+ to Fe2+, allowing it to
bind oxygen molecules more effectively.

3. **Oxygen Activation**:
- Molecular oxygen (O2) binds to the reduced form of the iron atom (Fe2+), forming a reactive
oxygen species known as an iron-oxo intermediate.
- This iron-oxo species is responsible for oxidizing the substrate in the subsequent steps.
4. **Substrate Oxidation**:
- The substrate interacts with the iron-oxo species, leading to the transfer of an oxygen atom
from the iron-oxo intermediate to the substrate.
- This results in the oxidation of the substrate and the formation of a metabolite.

5. **Product Release**:
- The oxidized product (metabolite) is released from the active site of the CYP450 enzyme.
- The enzyme returns to its original state, ready to catalyze another round of reactions.

6. **Regeneration**:
- NADPH-cytochrome P450 reductase regenerates the reduced form of the CYP450 enzyme by
transferring electrons from NADPH to the enzyme.
- This regeneration step completes the catalytic cycle of the CYP450 enzyme, allowing it to
continue metabolizing substrates.

Question 4
a. Describe how the following factors affect the action local anaesthetics
i. Lipid solubility [5]
ii. pH [4]
iii. Vasodilation [5]
**Factors Affecting the Action of Local Anesthetics**:

**i. Lipid Solubility**:

- **Effect**: Lipid solubility influences the penetration of local anesthetics through cell
membranes.
- **Explanation**: Local anesthetics must cross lipid-rich neuronal membranes to reach their
target site, the sodium channels. Higher lipid solubility enhances the ability of the anesthetic to
penetrate the membrane and reach its site of action, increasing its efficacy.
- **Clinical Impact**: Local anesthetics with higher lipid solubility typically have a faster onset of
action and require lower concentrations for effective anesthesia. Examples include bupivacaine
with high lipid solubility compared to lidocaine.

**ii. pH**:
- **Effect**: pH affects the ionization state of local anesthetics.
- **Explanation**: Local anesthetics exist in either ionized (charged) or non-ionized (uncharged)
forms. The ionized form (at high pH) is less able to penetrate the cell membrane, while the non-
ionized form (at low pH) is more lipid-soluble and can penetrate membranes efficiently.
- **Clinical Impact**: In areas with lower pH (e.g., inflamed tissues), local anesthetics exist
mostly in their non-ionized form, enhancing their membrane penetration and efficacy. Adjusting
the pH of the local anesthetic solution can optimize its action in different clinical scenarios.

**iii. Vasodilation**:
- **Effect**: Vasodilation influences the absorption and systemic distribution of local anesthetics.
- **Explanation**: Vasodilation at the injection site can increase the systemic absorption of local
anesthetics, leading to higher plasma levels and potentially systemic side effects. Conversely,
vasoconstriction can reduce systemic uptake and prolong the duration of action at the injection
site.
- **Clinical Impact**: Using vasoconstrictors like epinephrine with local anesthetics can reduce
systemic absorption, enhance local anesthesia duration, and decrease the risk of systemic
toxicity. However, caution is necessary in areas with compromised blood flow or where
vasoconstrictors are contraindicated.

b. Discuss the structure activity relationship of thyroid analogues in terms of

i. Bridging atom [3]
ii. 3’ and 5’ substitutions [5]
iii. Phenolic hydroxyl group [3]

**Structure-Activity Relationship of Thyroid Analogues**:

**i. Bridging Atom**:

- **Effect**: The bridging atom in thyroid analogues affects their biological activity.
- **Explanation**: The bridging atom, typically an oxygen atom in thyroid hormones like
thyroxine (T4) and triiodothyronine (T3), plays a crucial role in their interaction with thyroid
hormone receptors. The nature of the bridging atom affects the stability and binding affinity of
the analogue to the receptor.
- **Clinical Implication**: Modification of the bridging atom can lead to changes in the affinity
for thyroid hormone receptors and alter the pharmacological activity of the analogue.

**ii. 3’ and 5’ Substitutions**:

- **Effect**: Substitutions at the 3’ and 5’ positions of thyroid analogues influence their potency
and metabolic stability.
- **Explanation**: Substitutions at these positions can modulate the binding affinity to thyroid
hormone receptors, alter the metabolic pathways, and impact the duration of action of the
analogue in the body.
- **Clinical Impact**: Selective substitutions at the 3’ and 5’ positions can enhance the
pharmacokinetic profile and therapeutic efficacy of thyroid analogues, leading to improved
clinical outcomes in managing thyroid disorders.

**iii. Phenolic Hydroxyl Group**:

- **Effect**: The presence of a phenolic hydroxyl group in thyroid analogues affects their
receptor interaction and metabolic pathways.
- **Explanation**: The phenolic hydroxyl group in thyroid hormones is essential for receptor
binding and activation of downstream signaling pathways. Modifications to this group can alter
the affinity to thyroid hormone receptors and influence the biological activity of the analogue.
- **Clinical Implication**: Preserving the phenolic hydroxyl group or introducing specific
modifications can tailor the pharmacological properties of thyroid analogues, potentially
improving their therapeutic effectiveness and minimizing side effects.
Question 5.
ai. Using the structure of mechlorethamine hydrochloride and guanine, illustrate the mechanism
of DNA alkylation by nitrogen mustards. [6]

**Mechanism of DNA Alkylation by Nitrogen Mustards using Mechlorethamine Hydrochloride

and Guanine**:

Nitrogen mustards, such as Mechlorethamine Hydrochloride, are alkylating agents that form
covalent bonds with DNA, leading to DNA damage and disruption of cell division. Here is an
illustration of the mechanism of DNA alkylation by nitrogen mustards using Mechlorethamine
Hydrochloride and Guanine:

1. **Structure of Mechlorethamine Hydrochloride**:

- Mechlorethamine Hydrochloride (C5H11Cl2N) is an alkylating agent with a nitrogen mustard
group. It has a reactive nitrogen atom that can form covalent bonds with nucleophilic sites on
DNA.

2. **Structure of Guanine**:
- Guanine is one of the four nucleobases found in DNA. It contains sites susceptible to
alkylation, particularly the N7 position on the imidazole ring.

3. **Mechanism**:
- **Step 1 - Activation**: Mechlorethamine Hydrochloride is activated in an enzymatic or non-
enzymatic process to form an electrophilic species capable of alkylating DNA.

- **Step 2 - Alkylation**: The activated Mechlorethamine Hydrochloride reacts with the N7

position of Guanine in DNA. The nitrogen atom in Mechlorethamine acts as an electrophile,
attacking the nucleophilic nitrogen in Guanine, forming a covalent bond.

- **Step 3 - DNA Damage**: Covalent bonding between Mechlorethamine and Guanine alters
the structure of the DNA molecule. This modification inhibits proper base pairing, disrupts DNA
replication and transcription, and triggers cellular responses leading to cell death.

- **Step 4 - Repair or Apoptosis**: Cells may attempt to repair the damaged DNA using repair
mechanisms. If repair is unsuccessful, the cell may undergo apoptosis, programmed cell death, to
prevent the propagation of damaged DNA.

aii) What are 2 potential effects of DNA alkylation? [2]

aiii) Name an analogue of mechlorethamine, and explain how it improves on the prototypical
molecule? [3]

b. Which structure is necessary for intercalating activity of anti-tumour antibiotics? [3]

c. Name the species of bacteria doxorubicin and bleomycin were first isolated from? [2]
**aii) Potential Effects of DNA Alkylation**:
1. **DNA Crosslink Formation**: DNA alkylation can lead to the formation of crosslinks between
nucleotide bases, impairing DNA replication and transcription processes.
2. **Mutation Induction**: Altered DNA bases resulting from alkylation may lead to mutations
during cell division, potentially causing genetic abnormalities or contributing to the development
of cancer.

**aiii) Analogue of Mechlorethamine:**

- **Analog**: Chlorambucil
- **Improvement**: Chlorambucil, an analogue of Mechlorethamine, offers enhanced oral
bioavailability and improved tolerability compared to the parent compound. This modification
allows for more convenient administration and potentially reduced systemic toxicity.

**b. Structure Necessary for Intercalating Activity**:

- The flat, planar structure with aromatic rings is necessary for intercalating activity of anti-
tumour antibiotics. This structure allows the molecule to insert itself between adjacent base pairs
in the DNA double helix, disrupting DNA replication or transcription processes.

**c. Species of Bacteria for Doxorubicin and Bleomycin**:

- **Streptomyces**: Doxorubicin was first isolated from the bacterium Streptomyces peucetius,
while Bleomycin was initially discovered in the species Streptomyces verticillus. These bacteria
are known for producing various bioactive compounds, including these anti-tumour antibiotics
used in cancer treatment.

d. Anthracyclines generally have the structure presented below. Which R group(s) differ for
doxorubicin and daunorubicin? How do the functional groups differ? [3]

**Differences Between Doxorubicin and Daunorubicin in Anthracycline Structure**:

Anthracyclines, like doxorubicin and daunorubicin, share a common basic structure. The major
structural differences between these two drugs lie in their R groups. Here are the specific R group
differences and the functional groups that are altered between doxorubicin and daunorubicin:

1. **Doxorubicin**:
- **R Group Differences**: In doxorubicin, the R group consists of a **sugar moiety**,
particularly a **daunosamine** sugar.
- **Functional Group Differences**: The sugar moiety in doxorubicin contributes to its solubility
and stability. It affects the pharmacokinetics and pharmacodynamics of the drug.

2. **Daunorubicin**:
- **R Group Differences**: In daunorubicin, the R group comprises a **different sugar
moiety** known as **rhodomycin**.
- **Functional Group Differences**: The presence of the rhodomycin sugar in daunorubicin
alters its biological activity and some pharmacological properties compared to doxorubicin.

ei) What is the mechanism by which antimetabolites such as gemcitabine inhibit ribonucleotide
reductase, and which structural modification is required [4]

**Mechanism of Antimetabolites like Gemcitabine Inhibiting Ribonucleotide Reductase**:

Antimetabolites such as gemcitabine are chemotherapy drugs that interfere with nucleotide
metabolism in cancer cells. One of the key targets of gemcitabine is ribonucleotide reductase
(RNR), an enzyme responsible for converting ribonucleotides to deoxyribonucleotides, essential
for DNA synthesis. The mechanism by which gemcitabine inhibits RNR involves:

1. **Mechanism**:
- **Inhibition of Ribonucleotide Reduction**: Gemcitabine acts as a nucleoside analog that
undergoes intracellular phosphorylation to its active form, gemcitabine diphosphate.
- **Competitive Inhibition**: Gemcitabine diphosphate competes with the natural substrate,
deoxycytidine triphosphate (dCTP), for binding to the active site of ribonucleotide reductase.

2. **Structural Modification Required**:

- **Gemcitabine Triphosphate**: The active form of gemcitabine, gemcitabine triphosphate, is
the structural modification required for inhibiting ribonucleotide reductase effectively.
- **Modified Nucleoside Analog**: Gemcitabine, upon phosphorylation to its triphosphate
form, resembles the structure of deoxycytidine triphosphate but contains modifications that
disrupt the enzymatic activity of RNR.

ii) What is the active form of 5-fluorouracil? [2]

**Active Form of 5-Fluorouracil**:

The active form of 5-fluorouracil (5-FU) is **5-fluoro-2'-deoxyuridine-5'-monophosphate

(FdUMP)**. Once 5-FU is metabolized within the cell, it is converted into its active metabolite
FdUMP, which plays a crucial role in inhibiting thymidylate synthase, an enzyme involved in DNA
synthesis. By inhibiting thymidylate synthase, FdUMP disrupts the production of thymidine
monophosphate (dTMP), essential for DNA synthesis, and ultimately interferes with cancer cell
proliferation.

Question 6
a. State the structure activity relationship (S.A.R) of the compound below. [8]

b. Classify antiviral agents. Explain the mechanism of action and synthesis of one drug from 2
different classes [9]

**Classification of Antiviral Agents**:

Antiviral agents can be broadly classified into several categories based on their mechanism of
action and viral target. Here are common classes of antiviral drugs:

1. **Nucleoside/Nucleotide Analogs**: These compounds mimic natural nucleosides or

nucleotides and interfere with viral replication by inhibiting viral DNA or RNA synthesis. Examples
include acyclovir (herpesviruses) and tenofovir (HIV).

2. **Protease Inhibitors**: These drugs target viral proteases that are essential for the cleavage
of viral polyproteins into functional proteins, thereby inhibiting viral replication. Examples include
ritonavir (HIV) and boceprevir (Hepatitis C).

3. **Entry Inhibitors**: These agents block viral entry into host cells by targeting viral attachment
and fusion processes. Examples include enfuvirtide (HIV) and maraviroc (HIV).

4. **Neuraminidase Inhibitors**: These drugs target the viral enzyme neuraminidase, preventing
the release of new virions from infected cells and limiting viral spread. Oseltamivir (Tamiflu) and
zanamivir fall into this class, used for influenza.

**Mechanism of Action and Synthesis of Acyclovir (Nucleoside Analog) and Ritonavir (Protease
Inhibitor)**:

1. **Acyclovir**:
- **Mechanism of Action**: Acyclovir is a nucleoside analog that inhibits viral DNA synthesis by
acting as a chain terminator. Once phosphorylated by viral thymidine kinase, acyclovir
triphosphate competes with deoxyguanosine triphosphate for incorporation into viral DNA,
leading to chain termination and inhibition of viral replication.
- **Synthesis**: Acyclovir synthesis involves several steps. Initially, guanosine is converted to
acycloguanosine through a chemical modification process. Acycloguanosine is then further
phosphorylated to acyclovir monophosphate, which is subsequently converted to its active form,
acyclovir triphosphate, within the infected cells, enabling it to exert its antiviral effects.

2. **Ritonavir**:
- **Mechanism of Action**: Ritonavir is a protease inhibitor that binds to the active site of the
HIV protease enzyme, blocking its function. By inhibiting the cleavage of viral polyproteins into
functional proteins essential for viral maturation, ritonavir prevents the production of infectious
viral particles.
- **Synthesis**: The synthesis of ritonavir involves multiple chemical steps, including the
formation of key intermediates and the final assembly of the compound. The intricate process
culminates in the creation of ritonavir, which exhibits potent inhibitory activity against the HIV
protease enzyme.

c. Describe the types of drug receptor interactions of antilipidemic drugs. [8]

**Types of Drug-Receptor Interactions of Antilipidemic Drugs**:

Antilipidemic drugs are medications used to lower lipid levels in the blood, particularly
cholesterol and triglycerides. These drugs target various receptors and molecules involved in lipid
metabolism to reduce the risk of cardiovascular diseases. The types of drug-receptor interactions
of antilipidemic drugs include:

1. **HMG-CoA Reductase Inhibitors (Statins)**:

- **Type of Interaction**: Competitive Inhibition
- **Mechanism**: Statins inhibit the enzyme HMG-CoA reductase, a key regulatory enzyme in
the cholesterol biosynthesis pathway. By competitively binding to the active site of HMG-CoA
reductase, statins reduce cholesterol synthesis in the liver, leading to lower circulating LDL
cholesterol levels.

2. **Fibrate Agonists (PPAR-α Agonists)**:

- **Type of Interaction**: Agonism
- **Mechanism**: Fibrates activate peroxisome proliferator-activated receptor-alpha (PPAR-α),
a nuclear receptor that regulates lipid metabolism. PPAR-α activation increases the expression of
genes involved in fatty acid oxidation and reduces triglyceride levels in the blood.

3. **Bile Acid Sequestrants**:

- **Type of Interaction**: Non-receptor Mediated
- **Mechanism**: Bile acid sequestrants bind bile acids in the intestinal lumen, preventing
their reabsorption. This forces the liver to utilize circulating cholesterol to synthesize new bile
acids, leading to the lowering of LDL cholesterol levels.

4. **Cholesterol Absorption Inhibitors** (e.g., Ezetimibe):

- **Type of Interaction**: Inhibition
- **Mechanism**: Ezetimibe inhibits the NPC1L1 transporter in the small intestine, reducing
the absorption of dietary cholesterol. By blocking cholesterol uptake, ezetimibe lowers LDL
cholesterol levels in the blood.

5. **PCSK9 Inhibitors**:
- **Type of Interaction**: Neutralization
- **Mechanism**: PCSK9 inhibitors (such as evolocumab) neutralize proprotein convertase
subtilisin/kexin type 9 (PCSK9), a protein that degrades the LDL receptor. By blocking PCSK9,
these drugs increase the number of LDL receptors on the liver cells, promoting LDL clearance
from the bloodstream.

6. **Omega-3 Fatty Acids**:

- **Type of Interaction**: Modulation
- **Mechanism**: Omega-3 fatty acids, such as EPA and DHA, exert their effects by modulating
lipid metabolism and reducing triglyceride synthesis. They may also influence inflammatory
pathways and improve cardiovascular health.
Question 7
a. The figure below shows Thyroxine (T4). Describe the metabolism and excretion pathways of
this hormone. (15)

Fig. 1: Thyroxine (T4)

Thyroxine (T4) is a critical thyroid hormone that regulates various metabolic processes in the
body. The metabolism and excretion pathways of T4 are crucial for maintaining thyroid hormone
levels within the physiological range. Here is a detailed and precise description of the metabolism
and excretion pathways of thyroxine (T4):

1. **Metabolism of Thyroxine (T4)**:

- **Conversion to Triiodothyronine (T3)**: The primary metabolic pathway for T4 involves its
conversion to triiodothyronine (T3), the bioactive form of thyroid hormone. This conversion
occurs predominantly in peripheral tissues, such as the liver, kidney, and skeletal muscle, through
the action of deiodinase enzymes.
- **Deiodination Reactions**: Two main types of deiodinase enzymes are involved in the
conversion of T4 to T3: type 1 deiodinase (DIO1) and type 2 deiodinase (DIO2). These enzymes
catalyze the removal of an iodine atom from T4, generating T3, which has a higher affinity for
thyroid hormone receptors and is more biologically active.
- **Intracellular Transport and Action**: Once formed, T3 enters target cells and binds to
thyroid hormone receptors (THR) in the nucleus. This binding initiates gene transcription and
regulates cellular metabolism, growth, and energy expenditure.

2. **Excretion Pathways of Thyroxine (T4)**:

- **Renal Excretion**: Unbound T4 and its metabolites are filtered through the kidneys and
excreted in the urine. However, the majority of T4 is bound to carrier proteins like thyroxine-
binding globulin (TBG) and is not readily excreted, undergoing reabsorption and recycling in the
body.
- **Biliary Excretion**: A fraction of T4 can be excreted via the bile into the gastrointestinal
tract. In the gut, some T4 may undergo further metabolism or conjugation before being
eliminated in th feces.
- **Metabolism and Clearance**: T4 that is not converted to T3 or reverse T3 (rT3) may
undergo further deiodination or conjugation in the liver. Metabolites and unaltered T4 are
eventually cleared from the body through renal or biliary excretion pathways.

Describe the general structure-activity relationship of local anaesthetics. (10)

Fig. 1: Lignocaine HCL

The structure-activity relationship (SAR) of local anesthetics, such as Lidocaine (Lignocaine), is

crucial for understanding how changes in the chemical structure of these compounds impact
their anesthetic properties. Here is a detailed explanation of the general structure-activity
relationship of local anesthetics, focusing on Lidocaine HCl:

1. **Aromatic Ring**:
- Many local anesthetics, including Lidocaine, feature an aromatic ring in their structure. This
aromatic ring is often crucial for binding to specific sites on sodium channels in nerve cells,
blocking the influx of sodium ions and thereby inhibiting nerve conduction. Variations in the size
and substitutions on the aromatic ring can affect the potency and duration of action of the local
anesthetic.

2. **Amino Group**:
- Local anesthetics typically contain an amino group, which is essential for their interaction with
the sodium channels. The amino group may be tertiary, as in the case of Lidocaine, contributing
to the compound's potency by increasing membrane solubility and facilitating its penetration into
nerve cells.

3. **Ester or Amide Linkage**:

- Local anesthetics are classified based on their linkage to the aromatic ring, which can be an
ester (like procaine) or an amide (like Lidocaine). Amide-linked local anesthetics tend to have
longer durations of action and are more stable in biological environments compared to ester-
linked ones.

4. **Hydrophobic Tail**:
- The presence of a hydrophobic tail in local anesthetics, often attached to the aromatic ring,
impacts their potency and lipophilicity. This tail region helps the compound penetrate nerve cell
membranes and reach the site of action. Modifying the length or structure of the hydrophobic
tail can influence the local anesthetic's efficacy and duration of action.

5. **Stereochemistry**:
- The spatial arrangement of atoms in a local anesthetic molecule can significantly affect its
activity. Stereoisomers of a local anesthetic may exhibit varying affinities for sodium channels,
leading to differences in potency, duration of action, and side effect profiles.

6. **Ionization State**:
- The pKa of a local anesthetic determines its ionization state and influences its ability to cross
biological membranes. Local anesthetics need to be in their non-ionized form to pass through cell
membranes and reach their target sites within nerve cells effectively.

Question 8
a) Draw an illustrated diagram of insulin and describe how it work. [15]

Insulin is a highly sophisticated peptide hormone that plays a crucial role in regulating
metabolism, especially glucose metabolism, in the body. The advanced and precise mechanisms
of how insulin works can be outlined as follows:
1. **Mechanism of Insulin Secretion**:
- Insulin is synthesized and stored in pancreatic beta cells as preproinsulin and proinsulin. In
response to elevated blood glucose levels post-meal, glucose enters beta cells via GLUT2
transporters.
- Increased intracellular glucose levels lead to the closure of ATP-sensitive potassium channels,
causing depolarization of the cell membrane.
- Depolarization triggers the opening of voltage-gated calcium channels, allowing calcium influx
into the cell.
- Elevated calcium levels stimulate insulin granule exocytosis, releasing insulin into the
bloodstream.

2. **Insulin Signaling Cascade**:

- Insulin binds to its receptor, which is a receptor tyrosine kinase, initiating a complex signaling
cascade.
- Receptor autophosphorylation activates multiple downstream signaling pathways, including
the PI3K/Akt pathway and the MAPK pathway.

3. **Glucose Uptake and Glycogen Synthesis**:

- Insulin binding to its receptor activates the PI3K/Akt pathway, leading to the translocation of
GLUT4 transporters to the cell membrane.
- GLUT4 facilitates the uptake of glucose into muscle and adipose tissue, reducing blood glucose
levels.
- Once inside the cell, glucose can be used for immediate energy production or stored as
glycogen through glycogenesis, a process stimulated by insulin.

4. **Protein Synthesis and Growth**:

- Insulin activates protein synthesis pathways, such as the mTOR pathway, promoting the
synthesis of proteins essential for cell growth, repair, and function.
- It also inhibits protein breakdown, maintaining cellular protein balance and supporting tissue
growth.

5. **Lipid Metabolism and Lipogenesis**:

- Insulin influences lipid metabolism by promoting the storage of excess fatty acids as
triglycerides in adipose tissue through lipogenesis.
- It inhibits lipolysis, the breakdown of stored fats, thereby reducing the release of free fatty
acids into the bloodstream.

6. **Metabolic Homeostasis**:
- Overall, insulin plays a central role in maintaining metabolic homeostasis by regulating
glucose, protein, and lipid metabolism to ensure a balance of energy production, storage, and
utilization within the body.

Discuss three mechanisms for drugs that are used to treat Diabetes Mellitus (DM). In each case,
name the drug or class involved. [10]

1. **Insulin Therapy - Mechanism of Action and Drug Name**:

- **Mechanism**: Insulin therapy is a cornerstone in the management of Diabetes Mellitus
(DM), especially in Type 1 Diabetes where there is an absolute deficiency of insulin. Insulin
facilitates glucose uptake by cells, promotes glycogen synthesis, inhibits gluconeogenesis in the
liver, and regulates lipid metabolism. By mimicking the endogenous action of insulin, exogenous
insulin helps regulate blood glucose levels.
- **Drug Name**: Humalog (insulin lispro) is a rapid-acting insulin analog often used before
meals to control postprandial glucose spikes in patients with diabetes. It has a quicker onset of
action compared to regular insulin, making it suitable for managing blood sugar fluctuations
associated with meal consumption.

2. **Metformin - Mechanism of Action**:

- **Mechanism**: Metformin, a biguanide class of antidiabetic medication, is commonly
prescribed as a first-line treatment for Type 2 Diabetes. It primarily works by decreasing hepatic
glucose production and increasing insulin sensitivity in peripheral tissues. Metformin also
improves glucose uptake by cells and reduces intestinal glucose absorption, leading to lower
blood glucose levels.
- **Drug Name**: Metformin Hydrochloride (brand names: Glucophage, Glucophage XR) is a
widely used oral antidiabetic drug that helps control blood sugar levels by targeting multiple
aspects of glucose metabolism, making it an effective therapeutic option for Type 2 Diabetes
management.

3. **SGLT2 Inhibitors - Mechanism of Action and Drug Class**:

- **Mechanism**: Sodium-glucose co-transporter 2 (SGLT2) inhibitors are a class of antidiabetic
drugs that work by blocking the reabsorption of glucose in the kidneys, leading to increased
urinary glucose excretion. By promoting the elimination of excess glucose through urine, SGLT2
inhibitors help lower blood glucose levels and reduce hyperglycemia in patients with Type 2
Diabetes.
- **Drug Class**: Canagliflozin, dapagliflozin, and empagliflozin are examples of SGLT2
inhibitors commonly used in the treatment of Type 2 Diabetes. These drugs improve glycemic
control by a novel mechanism of action involving renal glucose excretion, offering an alternative
therapeutic approach for patients who may benefit from reducing glucose reabsorption in the
kidneys.

Question 10
a. Differentiate phase I and phase II Metabolic reactions, giving examples [8]

Phase I and Phase II metabolic reactions are essential processes in the body's metabolism,
dealing primarily with the modification and transformation of drugs and xenobiotics. Here are
more detailed differences and examples of each phase:
Phase I Metabolic Reactions:
- Definition: Phase I metabolism involves reduction, oxidation, or hydrolysis reactions that
convert lipophilic compounds into more water-soluble molecules for easier excretion.
- Characteristics:
- Phase I reactions add or expose a polar functional group (e.g., -NH₂ or -OH) to the substrate,
making it more hydrophilic.
- These reactions can activate, deactivate, or render a compound toxic.
- Predominantly occur in the liver, with the hepatic cytochrome P450 system being the primary
oxidation system.
- Examples:
- Oxidation: Involves the addition of oxygen to the molecule.
- Reduction: Involves the gain of electrons or a decrease in oxidation state.
- Hydrolysis: The cleavage of chemical bonds by water.

Phase II Metabolic Reactions:

- Definition: Phase II reactions involve conjugating the drug or its metabolites with another
molecule to enhance water solubility for elimination.
- Characteristics:
- Phase II reactions add hydrophilic groups to the compound, making it more readily excretable.
- Primarily serve as detoxification processes in metabolism.
- Follow Phase I reactions and aim to further modify the metabolites.
- Examples:
- Glucuronidation: Attachment of glucuronic acid to a substrate.
- Sulfation: Addition of a sulfate group (SO₃²⁻).
- Acetylation: Addition of an acetyl group (-COCH₃).
- Methylation: Addition of a methyl group (-CH₃).
- Conjugation with amino acids or glutathione.

b. Briefly outline how potency and efficacy can be optimized. [5]

Optimizing Potency:
* Understanding Quantal and Graded Dose-Response Curves: Potency refers to the amount of
drug needed to produce a given effect. It is often expressed as the quantal dose response ED50
or the graded dose response EC50. A highly potent drug evokes a larger response at lower
concentrations.
* Enhancing Receptor Affinity: Increasing the affinity of a drug for its target receptor can enhance
potency, as it allows the drug to produce a quantal effect in a larger proportion of the population
or achieve 50% of its maximal effect at lower doses.
* Chemical Optimization: Chemical modifications to the drug molecule can be explored to
improve its potency. This may involve altering the drug's structure to enhance its binding affinity
to the target receptor or to increase its bioavailability and tissue distribution.
Optimizing Efficacy:
* Maximizing Functional Response: Efficacy refers to the maximal effect that a drug produces
irrespective of concentration. Maximizing the drug's ability to produce a maximum functional
response is essential for optimizing efficacy.
* Receptor Activation: Enhancing the drug's ability to activate the target receptor and elicit a
maximal response while occupying a relatively low proportion of the receptors can optimize
efficacy.
* Therapeutic Effectiveness: While efficacy is important, it's also crucial to consider how well a
drug works in real-world use. Assessing a drug's effectiveness in clinical settings and patient
populations is essential for optimizing its therapeutic impact.

c. Discuss what causes attrition of drugs during preclinical and clinical trials [6]

The attrition of drugs during preclinical and clinical trials can be attributed to several factors,
impacting the success and progression of drug development. Here are the key causes identified
from the provided search results:
1. Safety Concerns and Cardiovascular Toxicity:
* Safety issues, including cardiovascular toxicity, represent a major cause of drug attrition
during preclinical and clinical development. Cardiovascular toxicity has been highlighted as a
significant concern, contributing to the withdrawal of medicines and impacting the duration of
drug therapies, particularly in the case of anticancer drugs .
2. Lack of Efficacy:
* Lack of efficacy in the intended indication has emerged as a major reason for late-stage drug
development failure. This is often established in randomized controlled clinical trials and can lead
to the discontinuation of drug candidates. The failure to demonstrate efficacy effectively indicates
that the target plays no role in the disease, leading to high rates of late-stage failure .
3. Preclinical Safety and Efficacy Testing:
* Preclinical and clinical safety concerns remain significant causes of drug attrition. Non-clinical
and clinical safety issues have been identified as major concerns during preclinical or clinical drug
development, influencing the progression of drug candidates into late clinical development and
marketing approval phases .
4. Inadequate Predictive Models:
* The need for more accurate prediction of the risk of drug-induced cardiotoxicity in preclinical
and early clinical stages has been emphasized. Inadequate predictive models for assessing the
risk of cardiovascular toxicity contribute to the progression of high-risk drug candidates into later
stages of development, leading to potential safety concerns and attrition .
5. Ethical and Regulatory Challenges:
* Ethical concerns related to animal testing in preclinical stages pose challenges, as some
individuals oppose such practices. Additionally, the design of clinical trials is based on the data
required by regulators, influencing the progression of drug development and the decision-making
process.

d. Prontosil, a sulfonamide derivative with the structure shown below, is inactive against
microorganisms in vitro, but shows activity in vivo. Explain why this is so and draw the structure
of the active compound derived from Prontosil [6]
 H
|
H--N--C6H5
|
H--S--O
|
H
Prontosil, a sulfonamide derivative, is initially inactive against microorganisms in vitro because it
is a prodrug. When ingested, it undergoes metabolic processes in the body that convert it into
the active form. The primary reason for its inactivity in vitro is that Prontosil itself lacks the
necessary chemical properties to inhibit bacterial growth directly. However, when it is
metabolized, it generates the active compound responsible for antimicrobial activity.

The active compound derived from Prontosil is sulfanilamide (4-aminobenzenesulfonamide). This

substance is formed in the body after the cleavage of the azo bond in Prontosil. Sulfanilamide
possesses the necessary structure to interfere with bacterial metabolic processes, particularly
folic acid synthesis, leading to its antimicrobial effects.

Question 9
a)Discuss any three (3) conditions that promote drugs entry into the Central Nervous System
(CNS). [10]

1. **Lipophilicity and Blood-Brain Barrier (BBB) Penetration**:

- **Lipophilicity**: Drugs with high lipophilicity have an advantage in crossing the blood-brain
barrier. The BBB is primarily composed of lipid-rich endothelial cell membranes that act as a
physical and biochemical barrier to many substances. Lipophilic drugs can easily diffuse through
these lipid layers, allowing them to penetrate the BBB and reach the brain tissue. This property is
particularly significant for drugs intended to target CNS disorders, as it ensures their access to the
brain, where their therapeutic effects are needed.

2. **Active Transport Mechanisms**:

- **Carrier Proteins**: Some drugs rely on active transport mechanisms to facilitate their
passage through the BBB. Specific carrier proteins present in the BBB actively transport certain
drugs across the barrier. By utilizing these transport systems, drugs can overcome the limitations
posed by the BBB's tight junctions and effectively enter the CNS. This targeted transport
mechanism enhances the therapeutic potential of these drugs for treating neurological
conditions.

3. **Molecular Size and Charge**:

- **Size and Charge**: The size and charge of a drug molecule significantly influence its ability
to penetrate the CNS. Smaller, uncharged molecules have a higher probability of crossing the BBB
compared to larger or highly charged compounds. Furthermore, drugs that are substrates for
efflux transporters like P-glycoprotein may encounter challenges in CNS entry due to active efflux
from the brain. Understanding the impact of molecular properties on transport mechanisms is
essential for designing drugs that can efficiently reach their targets within the CNS.

b) Benzylpenicillin is a narrow spectrum antibiotic. Discuss, illustrating and naming any three
changes to transform its activity to a broad spectrum antibiotic class. [15]

Benzylpenicillin, also known as penicillin G, is a narrow-spectrum antibiotic primarily effective

against Gram-positive bacteria. To transform its activity into a broad-spectrum antibiotic capable
of targeting both Gram-positive and Gram-negative bacteria, several modifications can be made.
Here are three key changes that can be implemented to enhance the activity of benzylpenicillin
and broaden its spectrum:

1. **Addition of a Beta-Lactamase Inhibitor**:

- **Illustration**: One modification to transform benzylpenicillin into a broad-spectrum
antibiotic is to combine it with a beta-lactamase inhibitor. Beta-lactamases are enzymes
produced by bacteria that can inactivate beta-lactam antibiotics, including penicillins. By
incorporating a beta-lactamase inhibitor like clavulanic acid or tazobactam, the antibiotic can
effectively overcome bacterial resistance mechanisms, thereby extending its spectrum of activity
to include beta-lactamase producing organisms such as many Gram-negative bacteria like
Escherichia coli and Klebsiella pneumoniae.

2. **Side Chain Modification**:

- **Illustration**: Changing the side chain of benzylpenicillin can alter its spectrum of activity.
For instance, by modifying the R-group of the penicillin molecule, semi-synthetic penicillins like
amoxicillin and ampicillin are created. These derivatives exhibit increased stability against beta-
lactamases and have enhanced activity against Gram-negative bacteria due to improved
penetration through the Gram-negative cell wall. This modification broadens the spectrum of the
antibiotic to include a wider range of pathogens.

3. **Structural Changes to Enhance Permeability**:

- **Illustration**: Structural modifications can enhance the permeability of the antibiotic across
bacterial cell membranes. For instance, introducing bulkier substituents or altering the molecular
structure to improve uptake into Gram-negative bacteria can lead to a broader spectrum of
activity. Modifications that enhance penetration through the outer cell membrane of Gram-
negative bacteria, such as alterations to the lipophilicity or size of the molecule, can enable the
antibiotic to effectively target these organisms in addition to Gram-positive bacteria.