This lecture discusses structure-activity relationships (SAR) and prodrugs. For SAR, analogs of lead compounds are synthesized with small modifications to identify important structural features for biological activity. Examining alcohol, phenol, aromatic, alkene, ketone, amine, carboxylic acid analogs can provide insights. The pharmacophore summarizes critical structural features. Prodrugs are inactive compounds converted in vivo to active drugs, addressing issues like permeability, toxicity, or sustained release. They include ester prodrugs for permeability and azathioprine for prolonged activity. Masking moieties can also reduce toxicity as in aspirin. Some prodrugs selectively release drugs at disease sites, like met

1. Lecture 5: Structure-Activity Relationship
and Prodrugs
Dr. Mohammed Khaled Bin Break

2. I. SAR

3. • Once the structure of a lead compound is known, the medicinal chemist moves on to study its structure–activity
relationships (SAR).
• The aim is to identify those parts of the molecule that are important to biological activity and those that are not.
• This is usually done by firstly synthesising analogues or derivatives of the lead compound. These analogues would usually
differ slightly from the parent lead compound, and this is done in order to know if the modified group is crucial for activity or
not.
• So basically the first step involves synthesising analogues where one particular functional group of the molecule is removed
or altered, in order to find out which groups are essential and which are not. The next step involves testing all the analogues
for biological activity and comparing them with the original compound. If an analogue shows significantly lowered activity,
then the group that has been modified must have been important. If the activity remains similar, then the group is not essential.
SAR

4. SAR
Example of SAR
determination
So, in this example,
analogues of the lead
compound X were
synthesised. As you
can see, a chemical
group was modified
each time in order to
see if it is important
for activity or not.
After screening all
these analogues, the
most important
groups for activity or
pharmacophores can
be identified. This is
called an SAR study.

5. • In this section, we would take a look on how to modify some functional groups that are often present in bioactive
compounds, in order to synthesise analogues and perform an SAR study.
SAR
BUT what groups should we use in synthesising our analogues?

6. • If we have a compound that contains an alcohol or phenol group, then one of the ways to examine whether the group is crucial
for activity or not, is to synthesise a methyl ether or an ester analogue of the parent compound.
• These analogues are usually the ones chosen for synthesis because they would disrupt the hydrogen bonding interaction that
would usually happen between the parent/lead compound and the receptor. The interaction gets disrupted due to the presence of
non-polar alkyl groups, so the added alkyl groups cannot act as hydrogen bond donors.
• So, after that, these analogues would be tested for their bioactivity. If activity was found to decrease then that means the presence
of the alcohol/phenol is crucial, and it also means that hydrogen bonding is an important interaction with the receptor that we
should not change. The opposite is true if the analogues’ activity was found to be similar.
SAR – Alcohols/Phenols

7. SAR – Alcohols/Phenols
Example of Alcohol/Phenol analogues
Methyl groups prevent hydrogen
bond donation

8. • Aromatic rings are planar, hydrophobic structures, commonly involved in van der Waals interactions with flat hydrophobic
regions of the binding site.
• For SAR studies, the flat aromatic ring could be replaced by a cyclohexane ring. Cyclohexane is a good substitute in this case
because it is NOT FLAT. The axial protons of the cyclohexane ring can interact weakly, but they also keep the rest of the
cyclohexane ring at a distance from the receptor resulting in weaker interactions. Bioactivity, as usual, would be also assessed
to see the effect of this substitution.
SAR – Aromatic rings

9. SAR – Aromatic rings
Binding comparison between an
aromatic ring and cyclohexyl ring
Axial protons

10. • Like aromatic rings, alkenes are planar and hydrophobic so they too can interact with hydrophobic regions of the binding site
through van der Waals interactions.
• For SAR studies, the flat alkene group could be replaced by an alkane. The saturated alkyl region is bulkier and cannot approach
the relevant region of the binding site so closely resulting in weaker interactions. Bioactivity, as usual, would be also assessed
to see the effect of this substitution.
SAR – Alkenes
Binding comparison between an alkene
and alkane group

11. • Ketones are usually found in a variety of medicinal drugs. It is a planar group that can interact with a binding site through
hydrogen bonding where the carbonyl oxygen acts as a hydrogen bond acceptor.
• The carbonyl group also has a significant dipole moment and so a dipole–dipole interaction with the binding site is also
possible.
• For SAR studies, the ketone could be reduced to an alcohol. This significantly changes the geometry of the functional group
from planar to tetrahedral. Such an alteration in geometry may well weaken any existing hydrogen bonding interactions and
will certainly weaken any dipole–dipole interactions, as both the magnitude and orientation of the dipole moment will be altered
• If it was suspected that the oxygen present in the alcohol analogue might still be acting as a hydrogen bond acceptor, then this
alcohol may be further converted to ether or ester analogues as described earlier in order to eliminate completely the effect of
hydrogen bonding interaction to ensure a successful SAR study.
SAR – Ketones

12. SAR – Ketones
Binding comparison between a
carbonyl and an alcohol

13. • Amines are very crucial in medicinal chemistry as they are present in a variety of drugs.
• They may be involved in hydrogen bonding, either as hydrogen bond acceptors or hydrogen bond donors. Tertiary amines
are an exception as they can act as hydrogen bond acceptors only, due to their lack of hydrogen atoms.
• For SAR studies, primary and secondary amine groups could be changed into amide groups in order to disrupt the hydrogen
bonding interaction that was present with the amines. The nitrogen group in amides can no longer act as hydrogen bond
acceptors, because its lone pair of electrons is now busy interacting with the adjacent carbonyl group.
• These amide analogues would be tested biologically in order to find if there is any change in activity compared to the amines.
SAR – Amines

14. SAR – Amines
This amide analogue still
has a proton that is capable
of donating hydrogen bonds
but the steric hindrance of R’
results in weakening or even
preventing any hydrogen
bond interactions. Nitrogen
here also cannot act as a
hydrogen bond acceptor as
explained earlier. This means
that hydrogen bonding has
been weakened.
This amide analogue has no protons, so
It cannot act as a hydrogen bond donor,
It also cannot act as a hydrogen bond
acceptor due to lack of unoccupied
lone pair of electrons as explained earlier.

15. • Carboxylic acids are quite common in drugs.
• They may be involved in hydrogen bonding, either as hydrogen bond acceptors or hydrogen bond donors.
• Carboxylic acid could also exist in its carboxylate ion state. This allows the possibility of an ionic interaction and/or a strong
hydrogen bond where the carboxylate ion acts as the hydrogen bond acceptor.
• For SAR studies, analogues such as esters, primary amides, primary alcohols and ketones could be synthesised and tested.
None of these functional groups can ionise, so a loss of activity could imply that an ionic bond is important.
The primary alcohol could shed light on whether the carbonyl oxygen is involved in hydrogen bonding, whereas the ester and
ketone could indicate whether the hydroxyl group of the carboxylic acid is involved in hydrogen bonding.
SAR – Carboxylic acids

16. SAR – Carboxylic acids
Carboxylic acid
derivatives

17. • Once we have completed our SAR study and established which groups are important for a drug’s activity, it is possible to move
on to the next stage, which is the identification of the pharmacophore.
• The pharmacophore summarises the important binding groups that are required for activity, and their relative positions in
space with respect to each other.
• So, if we finished the SAR study for compound X for example, and found that the two phenol groups, the aromatic ring, and the
nitrogen atom are important, then the pharmacophore would be represented as shown in the following slide.
Pharmacophores

18. Pharmacophores
It can be seen that pharmacophores may be represented as 2D or 3D. 3D pharmacophore specifies the relative positions of the
important groups in space. In this case, the nitrogen atom is 5.063 Å from the centre of the phenolic ring and lies at an angle of
18° from the plane of the ring. It can be also seen that it is not crucial to show the specific skeleton connecting the important
groups in 3D pharmacophore, and that makes it easier to compare directly the pharmacophores of different classes of drugs.

19. • Although pharmacophores are beneficial but they still possess some drawbacks.
• Pharmacophores focus too much on functional groups, but in reality, the overall skeleton of the molecule is involved in
interactions with the binding site through van der Waals and hydrophobic interactions. The strength of these interactions can
sometimes be crucial in whether a drug binds effectively or not, and the 3D pharmacophore does not take this into account.
• Pharmacophores also do not take into account the size of a molecule and whether it will fit the binding site.
Pharmacophores

20. II. Prodrugs

21. • Prodrugs are compounds which are inactive in themselves, but which are converted in the body to the active drug.
• They have been useful in tackling problems such as acid sensitivity, poor membrane permeability, drug toxicity, bad taste, and
short duration of action.
• Usually, a metabolic enzyme is involved in converting the prodrug to the active drug, and so a good knowledge of drug
metabolism and the enzymes involved allows the medicinal chemist to design a suitable prodrug which turns drug metabolism
into an advantage rather than a problem.
Prodrugs

22. • Some drugs have certain important functional groups for activity that may sometimes need to be ‘masked’ or hidden in order to
ensure that the drug crosses the cell membrane of the gut wall.
• For example, a carboxylic acid functional group may have an important role to play in binding a drug to its binding site via
ionic or hydrogen bonding. However, the very fact that it is an ionisable group may prevent it from crossing a fatty cell
membrane. The answer is to protect the acid function as an ester. The less polar ester can cross fatty cell membranes
and, once it is in the bloodstream, it is hydrolysed back to the free acid by esterases in the blood.
• Examples of ester prodrugs used to aid membrane permeability include enalapril, which is the prodrug for the antihypertensive
agent enalaprilate.
Prodrugs – Improving membrane
permeability

23. Prodrugs – Improving membrane
permeability
Example of a prodrug
ester

24. • Sometimes prodrugs are designed to be converted slowly to the active drug, thus prolonging a drug’s activity.
• For example, 6-mercaptopurine suppresses the body’s immune response and is, therefore, useful in protecting donor grafts.
However, the drug tends to be eliminated from the body too quickly. However, the prodrug azathioprine has the
advantage that it is slowly converted to 6-mercaptopurine by being attacked by glutathione, allowing a more sustained activity.
• Another approach to maintaining a sustained level of drug over long periods is to deliberately associate a very lipophilic group
to the drug. This means that most of the drug is stored in fat tissue from where it is steadily and slowly released into the
bloodstream. The antimalarial agent cycloguanil pamoate is one such agent. The active drug is bound ionically to an anion
containing a large lipophilic group and is only released into the blood supply following slow dissociation of the ion complex.
Prodrugs – Prolong activity

25. Prodrugs – Prolong activity
Conversion to mercaptopurine
via glutathione
cycloguanil pamoate

26. • Prodrugs can be used to mask the side effects and toxicity of drugs.
• For example, salicylic acid is a good painkiller, but causes gastric bleeding because of the free phenolic group.
This is overcome by masking the phenol as an ester (aspirin).
• The ester is later hydrolysed to free the active drug.
Prodrugs – Masking toxicity

27. • Prodrugs can be used to make certain drugs act at their most ideal location in the body.
• For example, Methenamine is a stable, inactive compound when the pH is more than 5. At a more acidic pH, however,
the compound degrades spontaneously to generate formaldehyde, which has antibacterial properties. This is useful in the
treatment of urinary tract infections.
• In the example above, formaldehyde was released exactly where it was needed which was at the infected urinary tract.
This is because the normal pH of blood is slightly alkaline (7.4) and so methenamine passes round the body unchanged.
However, once it is excreted into the infected urinary tract, it encounters urine which is acidic as a result of certain bacterial
infections. This acidic environment then causes the release of formaldehyde which then acts on the bacteria at the site of
infection.
Prodrugs – Drug targeting
Methenamine

28. Prodrugs
There are even further examples of
prodrugs, but we shall stop here!!!

29. THE END
ANY QUESTIONS?