1.6; 1.

9: a) The hormone adrenaline interacts with proteins

located on the surface of cells and does not cross the cell
membrane. However, larger steroid molecules, such as
estrone, cross cell membranes and interact with proteins
located in the cell nucleus. Why is a large steroid molecule
able to cross the cell membrane when a smaller molecule such
as adrenaline cannot?

b) Consider the structures of adrenaline, and estrone and

suggest what kind of intermolecular interactions are possible
for these molecules and where they occur.
The ability of a molecule to cross the fatty cell membrane has little to
do with its size, but more with its hydrophobic character.
Oestrone is more hydrophobic than adrenaline since it has a larger
carbon skeleton and only two polar functional groups. Thus, the
molecule is hydrophobic in character and can dissolve through the
fatty cell membrane.
Adrenaline has four polar functional groups and a much smaller carbon
skeleton. Thus, the polar functional groups dominate in determining
the character of the molecule making it very polar and unlikely to pass
through the cell membrane
There is another factor which makes it difficult for adrenaline
to cross the cell membrane. In aqueous solution, the four polar
groups will be highly solvated with water molecules. In order to
cross the cell membrane, these water molecules have to be
'stripped away' and this involves an energy penalty. The energy
of desolvation for oestrone would be less since it has only two
polar functional groups solvated.
 vdw vdw

vdw
2.3. Identify the intermolecular/intramolecular interactions that are
possible for the side chains of the following amino acids; serine,
phenylalanine, glycine, lysine, aspartic acid, and aspartate.
4.3. There are two main types of adrenergic receptor: the α and
β−adrenoceptors. Noradrenaline shows slight selectivity for the α-
receptor, whereas isoprenaline shows selectivity for the β-
adrenoceptor. Adrenaline shows no selectivity and binds equally
well to both the α- and β-adrenoceptors.
Suggest an explanation for these differences in selectivity.

Alpha stimulate the effector cells

Beta relax the effector cells
5.1. A model binding site for ATP was created for endothelial growth
factor (EGF) receptor kinase, which demonstrates how ATP is bound (see
above). Structure I is known to inhibit the binding of ATP. Suggest how
structure I might bind.

HBA
HBD

HBD HBA
7.2. Neostigmine is an inhibitor of acetylcholinesterase. The
enzyme attempts to catalyse the same reaction on neostigmine
as it does with acetylcholine. However, a stable intermediate is
formed which prevents completion of the process and which
results in a molecule being covalently linked to the active site.
Identify the stable intermediate and explain why it is stable.

HBA

ionic
HBA
7. 5. The methylation of cytosine
residues in DNA plays a role in the
regulation of transcription and is
catalysed by the enzyme DNA
methyltransferase. The mechanism is
shown as follows.

5-Azacytidine and 5-fluoro-2'-

deoxycytidine are mechanism-based
inhibitors of DNA methyltransferase.
Explain why.
 7. 7. The quinazoline structure shown is an inhibitor of the
enzyme scytalone dehydratase. One of the binding interactions
between the inhibitor and the active site is a hydrogen bond to
a water molecule, which acts as a hydrogen-bonding bridge to
two tyrosine residues. Explain why analogue I is three times less
active, whereas analogue II is 20 times more active

Analogue I is less active than the

original quinazoline as there is no
nitrogen to participate in the hydrogen
bonding network involving water and
two tyrosine residues. Moreover, the
additional hydrogen atom would clash
with the water molecule and displace
it. Therefore, there are fewer binding
interactions for analogue II, making it
a weaker inhibitor
- Analogue II has a nitrile substituent
which will also displace the water
molecule. However, the nitrile group
can form a hydrogen bonding
interaction directly to one of the
tyrosine residues. This binding
interaction must be stronger than the
original hydrogen bonding network
involving the quinazoline structure.
8. 1. Structure I is an agonist which binds to the cholinergic
receptor and mimics the action of the natural ligand
acetylcholine. Structure II, however, shows no activity and
does not bind to the receptor. Suggest why this might be the
case.
The three molecules are very similar to each other. Structures I and II differ from
acetylcholine in having an amino group and an ethyl group respectively instead of a
methyl group.

One might expect structure II to be active since a methyl and ethyl group are more
similar to each other than an amino group. Both are hydrophobic groups that can
interact by van der Waals interactions. In contrast, the amino group is a polar group
that is more likely to interact by hydrogen bonding. The fact that structure I is active
and structure II is inactive suggests that it is not binding that is crucial here and that
the difference in activity is due to the sizes of the different groups. The methyl and
amino groups are similar in size, whereas the ethyl group is larger. If the space
available in the binding site is limited, structure II may not fit due to the larger ethyl
group.
8. 2. Isoprenaline undergoes metabolism to give the inactive metabolite shown.
Suggest why this metabolite is inactive.
 The inactive metabolite has a methyl ether rather than a phenol
group. This indicates that the phenol group is an important
binding group when isoprenaline interacts with the adrenergic
receptor. For example, the hydrogen atom of the phenol group
may act as a hydrogen bond donor to a crroesponding hydrogen
bond acceptor in the binding site. This interaction is no longer
possible for the inactive metabolite.
Another possibility is that the phenolic oxygen acts as a hydrogen
bond acceptor and that the methyl group in the metabolite
prevents this interaction due to its size and bulk.
 8.4. Propranolol is an adrenergic antagonist. Compare the structure of
propranolol with noradrenaline and identify which features are similar in both
molecules. Suggest why this molecule might act as an antagonist rather than
an agonist, and whether it might show any selectivity between the different
types of adrenergic receptor

agonist (a substance that fully activates the receptor that it binds to) while under other conditions, behaves as an antagonist
(a substance that binds to a receptor but does not activate and can block the activity of other agonists).
The carbon bearing the alcohol group is an asymmetric centre has the same
configuration in each molecule. This is demonstrated by redrawing propranolol as
follows:

Therefore, it is possible for this moiety in both molecules to form similar

interactions with the receptor. However, the aromatic systems are different and
so different interactions are possible here, which can account for propranolol
acting as an antagonist rather than as an agonist if a different induced fit
results.
Propranolol is likely to show β-adrenergic selectivity due to the fact that it has a
bulky N-alkyl substituent
 8.6. Considering the interactions of oestradiol and raloxifene with the oestrogen
receptor (box 8.2) in order to answer this question.

Both oestradiol and raloxifene contain functional groups that can interact through
hydrogen bonding to the amino acids Glu-353, Arg-394 and His-524. Both molecule
have hydrophobic skeletons that position these groups correctly and match the
hydrophobic nature of the binding site. Oestradiol is an agonist whereas raloxifene is an
antagonist. This is due to the extra interaction with Asp-351 that is possible for
raloxifene.
8. 6. Tamoxifen acts as an antagonist for the estrogen receptor. Suggest
how it might bind to the receptor in order to do this.
11. 1. Benzene used to be a common solvent in organic
chemistry, but is no longer used because it is a suspected
carcinogen. Benzene undergoes metabolic oxidation by
cytochrome P450 enzymes to form an electrophilic epoxide
which can alkylate proteins and DNA. Toluene is now used as a
solvent in place of benzene. Toluene is also oxidized by
cytochrome P450 enzymes, but the metabolite is less toxic and
is rapidly excreted. Suggest what the metabolite might be and
why the metabolism of toluene is different from that of
benzene.
11. 1) In contrast to benzene, toluene has an accessible methyl
group which can be manipulated easily by metabolic enzymes.
Exposed methyl groups are susceptible to oxidation, and so the
most likely metabolite is benzoic acid which could undergo
further phase II conjugation reactions and be quickly excreted
11.2. The prodrug of the antipsychotic drug fluphenazine shown
below has a prolonged period of action when it is given by
intramuscular injection, but not when it is given by intravenous
injection. Suggest why this is the case
Fluphenazine contains
an ester group which is
susceptible to hydrolysis
by esterases in the
blood. If the drug is
given by i.v. injection,
the ester is quickly
hydrolysed. If the ester
is given by
intramuscular injection,
it takes longer for it to
enter the blood supply
and so its rate of
hydrolysis is slower (see
also section 14.6.2).
11. 3. Morphine binds strongly to opioid receptors in the brain
to produce analgesia. In vitro studies on opioid receptors show
that the quaternary salt of morphine also binds strongly.
However, the compound is inactive in vivo when injected
intravenously. Explain this apparent contradiction.
3) The quaternary salt of morphine contains a permanent
positive charge. If the compound is administered in vivo, it has
to cross the blood brain barrier in order to reach the analgesic
receptors in the brain. However, the blood brain barrier is
hydrophobic, and since the compound has a permanent
positive charge, it cannot cross. Thus, the observed inactivity in
vivo is due to the inability of the compound to reach the
receptors in the brain.
In vitro tests are carried out on isolated receptors or cells and
so there is no blood brain barrier to cross
11. 4. The phenol group of morphine is important in binding
morphine to opioid receptors and causing analgesia.
Codeine has the same structure as morphine, but the phenol
group is masked as a methyl ether. As a result, codeine binds
poorly to opioid receptors and should show no analgesic activity.
However, when it is taken in vivo, it shows useful analgesic
properties. Explain how this might occur.
4) When codeine is administered, a certain proportion of it
undergoes a metabolic reaction in the liver which results in
the removal of the methyl ether and generation of
morphine. This accounts for the analgesic activity observed
11. 6. A drug contains an ionized carboxylate group and shows
good activity against its target in in vitro tests. When in vivo
tests were carried out, the drug showed poor activity when it
was administered orally, but good activity when it was
administered by intravenous injection. The same drug was
converted to an ester, but proved inactive in vitro. Despite that,
it proved to be active in vivo when it was administered orally.
Explain these observations
In vitro studies show that the drug has good activity against is target. The fact
that the drug shows poor activity when it is administered orally can be put
down to poor absorbtion from the digestive tract. Since the drug has a highly
polar carboxylate group present, it will not pass through the hydrophobic cell
membranes of the cells lining the gut wall.
If the drug is administered by intravenous injection, it is introduced directly
into the blood supply and can now each its target.
The ester of the drug acts as a prodrug. When administered orally, the prodrug
can cross the cell membranes of the cells lining the gut wall since the ester
masks the polar carboxylate group. Once the prodrug is in the blood supply,
esterases hydrolyse the ester to unmask the carboxylate group and the drug
can interact with its target.
The prodrug itself is inactive when tested in vitro since the carboxylate group is
masked. This indicates that the carboxylate group is an important binding
group.
11. 7. Atomoxetine and methylphenidate are used in the treatment
of attention deficit hyperactivity disorder.
Suggest possible metabolites for these structures.
There are a variety of possible metabolites based on the groups
present. The following are some possible metabolic reactions.

CH2OH -> CH=O

=> COOH
Phase 2 at
CH2OH or COOH
Various possible metabolites include the following for
methylphenidate:
for atomoxetine:
11. 8. Suggest metabolites for the proton pump inhibitor
omeprazole.
The following are just a few examples of the many possible
metabolites. Note that more than one metabolic reaction may
occur on the one molecule.