This document discusses the effects of substituents on the structure-activity relationships of molecules. It focuses on methyl, alkyl, unsaturated, and halogen substituents. Methyl groups can increase lipophilicity and solubility while also inducing conformational and electronic effects. Larger alkyl groups have similar but amplified effects. Unsaturated groups introduce geometric isomers and reactivity while facilitating metabolism. Halogens like fluorine provide electronic, hydrophobic, and steric effects useful for bioactivity and evading metabolism. Overall, substituents can profoundly modify a molecule's potency, duration, and pharmacological properties.

1. Substituents and Functions:
Qualitative and Quantitative
Aspects of Structure–Activity
Relationships
Substituent Groups

2. I. INTRODUCTION
The replacement, in an active molecule, of a
hydrogen atom by a substituent (alkyl,
halogen, hydroxyl, nitro, cyano, alkoxy,
amino, carboxylate, etc.) or a functional
group can deeply modify
The potency,
The duration,
Perhaps even the nature of the
pharmacological effect.

3. II. METHYL GROUPS
• In this section, we show how a methyl group, so often
considered as chemically inert, is able to alter deeply the
pharmacological properties of a molecule.
We will envisage successively effects on
 the solubility,
 conformational effects,
 electronic effects and effects on the bioavailability and
the pharmacokinetics.
In the last paragraph, we will present some replacement
possibilities of the methyl groups by related groups and
extend the study to some larger alkyl groups.

4. A. Effects on solubility
1. Increase in lipophilicity
CH3 gives place to a positive log (P)
increment of 0.52
• The increase in lipophilicity due to
methylation can drastically modify the
bioavailability of the drug, and thus its
efficacy i.e increased affinity for the
receptor.

5. 2. Hydrophobic interactions
• As stated above, the usual result of the methyl group addition
to a given molecule is to augment its lipophilicity:
• There are, however, exceptions to this rule, especially when the
grafting of one or several methyl groups can render the
molecule more compact (more “ globular ” ).
A good illustration of this effect is provided by aliphatic alcohols.
5+
A lesser amount of structured water molecules is needed
to wrap a compact molecule (2,2,3-trimethylbutane) than to
wrap an extended one ( n -heptane).

6. 3 .Crystal lattice cohesion
 Greater water solubility can also result from a decrease of
the crystal lattice energy, the methyl groups hindering the
various intermolecular interactions (hydrogen bonds,
dipole–dipole bonds, etc.).
 In the antibacterial sulfonamide series, The substitution of
the pyrimidine ring of sulfadiazine by one, then two, methyl
groups causes an increase in solubility.
 one would expect why the methyl substituted derivatives
are less soluble. This for the double reason that they show
increased lipophilicity and that they are less dissociated
than the parent molecule.
N
N
NH2 SO2NH
CH3
CH3
N
N
NH2 SO2NH
Sulfamidine Sulfadiazine

7. Indeed the inductive character of the methyl
groups disfavors ionization and the non-
ionized form of a molecule is always less
soluble than the corresponding ionized
form.
Despite this unfavorable electronic effect,
sulfamidine is approximately five times
more soluble than sulfadiazine.
N
N
NH2 SO2NH
CH3
CH3
N
N
NH2 SO2NH
Sulfamidine Sulfadiazine

8. B. Conformational effects
The steric hindrance generated by a methyl
group can create constraints and impose
particular conformations that may be
favorable or unfavorable for ligand–receptor
interactions.

9. C. Electronics effects
The methyl group and, more generally all alkyl
groups, are the only substituents acting by an
inductive electron-donating effect.
All the other groups are electron donors by
mesomeric effects.
This means that the methyl and the alkyls are
electron donors in any environment while a basic
group, dimethylaminoethyl for example, will be
a mesomeric donor in basic or neutral medium,
but will become strongly electron attracting by
protonation in gastric medium (pH 2).

10. D. Effects on metabolism
Seen from the metabolic point of view the
methyl group plays a particularly important
role.
Three possibilities are currently met:
(a) the methyl group is oxidized,
(b) the methyl group is shifted and
(c) the methyl group is not (or only slightly)
attacked and can then serve as blocking
group.

11. 1.Oxidation of the methyl group
The oxidation of the methyl group begins generally with
the formation of the hydroxymethyl analog and continues
usually until the carboxyl step.
This is observed for simple compounds like camphor or 2-
methyl-pyridine but also for drugs like tolbutamide,
explaining the relatively short half-life of these latter
compounds.
Sometimes the oxidation of the methyl group gives rise
to an active metabolite, contributing thus to a reasonable
half-life to the drug.
The grafting of a methyl group, especially on aromatic
rings, represents often a good mean of detoxification.

12. 2.The methyl group is shifted
• A methyl group, when grafted on a nitrogen or sulfur
atom, can transform this latter in an “ onium, ” able to act
as methyl donor. In living organisms the usual suppliers of
methyl rests are choline and methionine.
• More generally, any S - or N -methylated drug can
constitute a methyl donor.
• On the other hand, when the methyl (or alkyl) rest is
linked to a good leaving group, as found for alkyl sulfates
or sulfonates such as methyl sulfate or busulfan,
alkylating reagents are produced and there exists a huge
risk of carcinogenicity.

13. 3.The methyl serves to block a
reactive function
A reactive function, such as an active hydrogen
belonging to a hydroxyl, thiol or amino, can be
masked by methylation.
Methyl groups can thus serve to protect sensitive
functionalities from metabolic hydroxylation.
The ene-diol function is essential to the antioxidant
properties of vitamin C, it is therefore not
surprising that its methylation leads to an
inactive compound

14. • In steroids the 6α-position (e.g. prednisolone is a
position that is normally hydroxylated. Grafting a
methyl in this place prevents its hydroxylation.
• Halogens (particularly fluorine) suit even better
because they are not sensitive at all to oxidative
attacks.
O
O
OH
CH3
OH
CH3
OH O
O
OH
CH3
OH
CH3
OH
CH3
Prednisolone
Methylprednisolone

15. E. Extensions to other small
alkyl groups
• The methyl group is the prototype of a
saturated aliphatic substituent with lipophilic
and electron-donor inductive effect.
• In some instances, it can advantageously
be replaced by related groups bringing
either symmetry, or more lipophilicity, or an
increased inductive effect.

16. bulkiness ( E s ) of the isopropyl and
cyclopentyl groups, while the tert-butyl
group is far more voluminous.
Furthermore, it is remarkable to observe that
the electron-donor effect of the cyclopentyl
group is superior to that of the cyclohexyl
group.

17. 2.Gem -dimethyl and spiro-
cyclopropyl
• Gem -dimethyl and spiro-cyclopropyl are useful to
render a carbon atom quaternary and therefore
resistant to metabolic attacks.
O
O
OH
O
OH
CH3 CH3
CH3
CH3
Gemeprost (abortifacient)

18. Gem -dimethyl can also constitute solutions
to introduce symmetry into a chiral center,
or to protect a close and sensitive
function, as in the case of gemeprost, an
analog of prostaglandin E1 used in medical
abortion, where the gem - dimethyl groups
at C-16 protect the alcohol moiety at C-15
from rapid metabolic oxidation.

19. 3.Isopropyl and cyclopropyl
The cyclopropyl rest is less bulky than the isopropyl group
for a maximal electron-donor effect.
This electronic effect is involved when the cyclopropyl
group of efavirenz, a nonnucleoside reverse
transcriptase inhibitor, interacts with the aromatic ring of
tyr181 via a π-aryl interaction which is presumably
favorable to binding.
The lipophilic effect of cyclopropyl explains why abacavir, a
nucleoside reverse transcriptase inhibitor, has
an improved absorption in the CNS compared to
diaminopurine dioxolane (DAPD).

20. 4. The cyclopentyl group
The cyclopentyl group creates the maximal inductive effect
for a relatively reasonable bulkiness. It is often a good filling
of a hydrophobic pocket as illustrated for the cAMP.
Phosphodiesterase inhibitor rolipram .
The inhibitory activity toward type IV cAMP
phosphodiesterase is increased 10 times when the meta
-methoxy group is replaced by a meta -cyclopentyl group
(rolipram).
N
H
O
O
O
CH3
N
H
O
O
O
CH3
CH3
Rolipram

21. III. EFFECTS OF UNSATURATED
GROUPS
1. Existence of electronic effects : the unsaturated rests
behave as electron attractors through inductive effects.
Furthermore, direct interactions of donor–acceptor type
are possible thanks to the π electron cloud surrounds
present in multiple bonds.
2. Possibility of existence of a geometrical isomery
(e.g. cis – trans geometric isomery).
3. Possibility of activation through conjugation :
the association of several unsaturated functions in
conjugated position (dienes, enynes, enones, enolides,
polyunsaturated derivatives) renders the corresponding
molecules very reactive. It facilitates especially the
addition of biological nucleophiles and notably of thiols.

22. 4. Facilitation of the metabolism :
The unsaturated element constitutes often the vulnerable
site of the molecule, that will be attacked first (e.g. by
formation of an epoxide that evolves into a diol that, on
its turn, can undergo oxidative cleaving), but this is not
always the case. Therefore, one should pay attention to
the problems posed by the formation of these
metabolites (aldehydes, carboxylic acids … ): they can
also be biologically active.
5. Increase of the narcotic power and the toxicity in
comparison with the corresponding saturated
compound.
Ethylene, acetylene, trichlorethylene, divinyl oxide and,
by extension, cyclopropane are examples of unsaturated
narcotics

23. Classification of unsaturated
groups
• A. Vinyl series
• B. Allylic series
• C. Acetylenic series
• D. Cyclenic equivalents of the phenyl
ring

24. Classification of unsaturated
groups
A. Vinyl series
• It may take part to a beneficial electronic interaction.
B. Allylic series
• All allylic derivatives are relatively hepatotoxic and
irritant.
• Allylic alcohol itself serves to create experimental hepatic
lesions that allow testing hepatoprotecting drugs.
We will envisage three categories of allylic derivatives:
 C –allyl derivatives,
 N -allyl derivatives,
 and O -and S -allyl derivatives which often possess
alkylating properties.

25. 1- C -allyl derivatives
They present the double advantage to be
lipophilic (rapid onset) and to give place to
fast biodegradation (short duration of
action). However, they often conserve the
intrinsic hepatotoxicity of the allyl group.
• Allobarbital is a sedative hypnotic that is
no longer used; allylestrenol acts as a
pure progestative hormone and alprenolol is
a β -blocker

26. 2.N -allyl derivatives
The replacement in morphine, and in some
of its simplified analogs, of the N -methyl
group by a N -allyl group (and, later on, by
some related groups) has constituted a
decisive step in the study of opiate
analgesics.
Indeed this modification had for the first time
achieved the passage of morphinic
receptor agonists to the corresponding
antagonists

27. O - and S -allyl derivatives
• Alkylating allyl derivatives: When the allyl rest
bears
• a good leaving group, it generates easily the
allylic cation.
• This cation is stabilized by mesomery, and is an
excellent electrophile.
• Many natural compounds can release allylic
alcohols. A first example is found in allicine, the
antibacterial principle of garlic, which results
from the action of alliinase on alliine.
• Penicillin O and penicillin S are both S -allyl
derivatives.

28. C. Acetylenic series
1. Electronic effects
• The acetylene function exerts an
electron-attracting effect. This effect can
be reinforced by substitution of the
acetylenic hydrogen.
• The acetylenic CH can act as an
hydrogen bond donor

29. 2. Aromatic ring equivalents
Thanks to their π electron clouds and to their
small volume, ethynyl groups can
sometimes function as bioisosteres
of aromatic rings and give similar donor–
acceptor interactions.
• Acetylenic group has the rapid
metabolization of ethynyl groups

30. 3.Structural constraints
• In inserting an acetylenic function between
two carbon atoms, one achieves a
structure with four “ on-line” atoms
representing a rigid entity with a distance
of 4.2 Å between the two extreme atoms

31. D. Cyclenic equivalents of the
phenyl ring
 The cyclohexenyl ring and, to a lesser extent the
cyclopentenyl and cycloheptenyl rings can
possibly replace a phenyl ring.
 This is the case for the barbiturics cyclobarbital
and heptabarbital which are entirely comparable
to phenobarbital.
 From the metabolic point of view, the
cyclohexenyl ring is oxidized in position α to the
double bond to produce the corresponding
cyclohexenone

32. IV. EFFECTS OF HALOGENATION
A. The importance of the halogens in the
structure–activity relationship
1. Steric effects
The obstruction of a molecule by means of
halogen substitution can impose certain
conformations or mask certain functions.
In the case of clonidine the bulky halogen atoms
prevent the free rotation and maintain the planes
of the aromatic rings in a perpendicular position
to each other.

33. 2. Electronic effects
• Halogens have negative inductive effect
which is in the following order:
F > Cl > Br > I
• The mesomeric donor effect of the
halogen atoms is usually not involved in
biological medias.

34. 3-Hydrophobic effects
• Halogen have lipophilic effect.
π of F = 0.14, Cl = 0.71, Br = 0.86, and CF3 = 0.88
4- Reactivity of the halogens
• In terms of bond strength, all C-halogen bonds
are weaker than the C — H bond except for the
C — F bond, due to the high electronegativity of
the fluorine and an orbital size similar to that of
carbon.

35. B. Usefulness of the halogens and of
cognate functions
1- Fluorine
It induces an increase in lipophilicity and its
electronegativity is the highest in the periodic
classification.
The difference in electronegativity between fluorine
and carbon creates a large dipole moment in this
bond.
This dipole may contribute to the molecule’s ability
to be engaged in intermolecular interactions.

36. • Fluorine is able to participate to hydrogen bonds
with the hydrogen of water.
These bonds are weaker than those obtained with
oxygen, but they are still strong enough to
contribute to the binding of fluoroaromatic
compounds to active site and/or receptor
• The importance of electrostatics in the
interaction of aromatics fluorine with cations and
hydrogen bond donors can be visualized using
electrostatic potential surfaces

37. In monofluorobenzene, the potential of the
fluorine is concentrated on the unique
fluorine present, whereas in
polyfluorobenzene the negative charge is
spread over several fluorine atoms. For
this reason, monofluorobenzene may give
stronger interactions.
• Fluorine is also used to block
metabolically sensitive positions of a
molecule. When the fluorine is placed in
an activated position.

38. 2-Chlorine
A chlorine substituent produces simultaneously an
increase in lipophilicity, an electron-attracting
effect and a metabolic obstruction.
3- Bromine
Bromine is the less used halogen, and when it
serves, it is usually incorporated as a bromo-
aryl. The reproach against bromine is to
generate reactive alkylating intermediates,
more easily than chlorine or fluorine.

39. 4-Iodine
• Although even lesser tolerated than bromine, iodine is
used to the treatment of certain thyroidal deficiencies.
Administrated by internal route, iodine and iodine
derivatives
• trigger either acute hypersensitivity reactions (larynx
oedema, cutaneous hemorrhages, fever, arthralgies,
etc.). chronic reactions (iodism).
• In addition to its use in certain dysfunctions of the thyroid
gland, iodine presents to specific uses: covalent iodine
derivatives serve as radiological contrast substances and
131 iodine (half-life: 8 days) is used as radioactive
tracing agent.

40. 5-Extensions-cognate groups
• Chlorine, trifluoromethyl, cyano or azido
groups are more or less bioisosteres.
• Other possible candidates are: SCN,
SCF3 , -SO2CF3 and CH =CF2

41. V. EFFECTS OF HYDROXYLATION
A. Effects on solubility
• The introduction of an alcoholic or a
phenolic hydroxy group into an active
molecule changes the partition coefficient
toward more hydrophilicity and renders
the molecule more water soluble.

42. B. Effects on the ligand–receptor
interaction
• The hydroxy group is an essential element
for hydrogen bonding with the receptor.
For others the attachment of a hydroxy
group can result in potency changes.
Beta receptor agonistic activity of
epinephrine and desoxyepinephrine.

43. C. Hydroxylation and metabolism
As a rule metabolic hydroxylation of an
active compound represents a
detoxication (phase I) mechanism. It
results generally from a first-pass effect
and can be followed or not by a
conjugation reaction.

44. VI. EFFECTS OF THIOLS AND OTHER
SULFUR-CONTAINING GROUPS
A. Drugs containing thiol:
They are able to coordinate Zn(II) and act as free radical
scavenger.
Their lipophilicity allows them to attain high lever in heart
tissue and then they can be used as cardioprotective drugs
The heavy-metal chelating properties of thiols were taken
advantage of in the design of dimercaprol ( “ British Anti-
Lewisite, ” BAL) as counter poison of the arsenical war gas
Lewisite.
Methylthio substitution on aromatic rings is practiced, but
even then, the obtained thioethers are very reactive.
They are easily converted to sulfoxides and vice versa

45. B. Drugs containing oxidized sulfides
The sulfoxide (S=O) and the sulfone (O=S=O)
functions are very polar and usually confer
mediocre CNS bioavailability.

46. VII. ACIDIC FUNCTIONS
The prototypical representatives of the group are the
carboxylic acids. However, a huge number of
bioisosteres such as sulfonic or phosphonic acids,
tetrazoles or 3-hydroxyisoxazoles are available
R
PO OH
OH
N
O
OH
R
S OO
OH
NH
N
N
N
R
O
OHR

47. A. Effects on solubility
• Carboxylic acids are often highly ionized
at the physiological pH values and this is even more the
case for sulfonic acids and poorly cross membranes.
• They are subject to a rapid clearance from the animal
body.
• However, once absorbed, they can establish strong
ionic interactions with the basic amino acids, especially
with lysine, contained in the blood serum albumin, or the
enzyme and receptor proteins.

48. • The second generation of antihistaminic
compounds are less lipophilic, thanks to the
replacement of the hydroxy group by a carboxylic
acid. They are also P-gp substrate, which limits
CNS exposure.
N N
Cl
OH
O
N N
Cl
O
COOH
Hydroxyzine
Cetirizine

49. B. Effects on biological activity
• The sulfonic acids as a class are generally
not biologically active.
• For carboxylic acids the situation depends on
whether the carboxylic function is introduced in
small or large molecules.
1. In small molecules
• The introduction of a carboxylic group changes
fundamentally the biological activity. Very often
the initial biological activity is destroyed and
the toxicity of the parent compound is reduced.

50. .
NH2
NH2
COOH
OH
OH
COOH
Phenethylamine Phenylalanine
(inactive as sympathomimetic)
Phenol (no antiinflammatory)
2. In large molecules:
High pharmacological activity is maintained
despite the presence of the carboxylic group.

51. 3-Isosteric substititution of carboxylic
group
• A good example is
losartan.
• Activity increases
dramatically by
substituting carboxylic
group by tetrazole. R pKa IC50(nM)
COOH 5 0.23
COONHSO2P
h
8.44 0.14
NHCOCF3 9.5 6.3
NHSO2CF3 4.5 0.083
Tetrazole 5–6 0.019
N
N
nBu
Cl
OH
R

52. VIII. BASIC GROUPS
The basic groups met in medicinal chemistry are
the amines, the amidines, the guanidines and
practically all nitrogen containing heterocycles.
Basic groups are polar and one would expect that
highly ionized bases (especially quaternary
ammonium salts) would resemble the sulfonic
acids and show limited activity due to their
mediocre membrane permeability.
In practice bases with p K a values superior to 10
have very limited chance to reach the CNS.

53. • As seen for the acidic groups, the introduction of
a basic group into a biologically active compound
which contains no such group already has as
consequence essentially a solubilizing effect.
This effect can also be enhanced through salt
formation.
• In drug–protein interactions the classical counter-
anions of organic bases are the aspartic and the
glutamic carboxylates.

54. • Acylation deactivates the amines strongly
as does the introduction in some other
place of the molecule of a carboxylic or
sulfonic group (formation of zwitter ions:
bipolar ions).
• Aromatic amines are always more
hazardous than aliphatic amines and form
toxic metabolites

55. IX. ATTACHMENT OF ADDITIONAL
BINDING SITES
A. To increase lipophilicity
Cyclic amino acids such as nipecotic acid and guvacine have
been shown to inhibit GABA uptake (anticonvulsant).
However, these small amino acids do not readily cross the
BBB and thus limit their potential clinical usefulness. A
considerable improvement has been the discovery of
compound SKF 89976A
COOH
NH
COOH
N
COOH
NH
Nipeconic
acid
Guvacine SKF 89976A

56. B. To achieve additional interactions
• The fixation of large aromatic substituents
such as 2-naphtyl and 3,3-diphenylpropyl
to the low-efficacy partial agonist 4-PIOL
transform this series in powerful GABA A
receptor antagonists.

57. Instead of ensuring high lipophilicity, these aralkyl
groups serve to achieve additional interactions
with the target macromolecule.
This is typically the case for the angiotensin
converting enzyme inhibitor enalaprilat. The
exchange in captopril of the thiol function for a
carboxylic group as ligand for the enzyme zinc
atom entails an important decrease in activity.
This decrease could be compensated by the
attachment of a phenethyl moiety.
N
O O
OH
SH CH3
H N
NH
O
O
O
OH
O
CH3
CH3
H H

58. For further readings:
Camille Wermuth David Aldous Pierre
Raboisson Didier Rognan
“The practice of Medicinal Chemistry”
Academic press