Advanced Medicinal

Chemistry
Lectures 6 and 7:
Physical Properties and Drug
Design

Rhona Cox
AstraZeneca R&D Charnwood
 Overview
Introduction
Ionisation

Lipophilicity
Hydrogen bonding
Molecular size Two lectures

Rotatable bonds
Bulk physical properties

Lipinski Rule of Five

The Drug Design Conundrum
 What must a drug do other than bind?
An oral drug must be able to:
dissolve
survive a range of pHs (1.5 to
8.0)
bladder survive intestinal bacteria
cross membranes
kidneys survive liver metabolism
BBB
avoid active transport to bile
avoid excretion by kidneys
partition into target organ
bile
avoid partition into undesired
duct
places (e.g. brain, foetus)

liver
 Why are physical properties
important in medicinal chemistry?
So, before the drug reaches its active site, there are many hurdles
to overcome.

However, many complicated biological processes can be modelled

using simple physical chemistry models or properties and
understanding these often drives both the lead optimisation and
lead identification phases of a drug discovery program forward.

This lecture will focus on oral therapy, but remember that there are
lots of other methods of administration e.g. intravenous, inhalation,
topical. These will have some of the same, and some different,
hurdles.
 Reducing the complexity
Biological process in Underlying physical Physical chemistry
drug action chemistry model

Energy of dissolution;
Dissolution of drug in Solubility in buffer,
lipophilicity & crystal
gastrointestinal fluids acid or base
packing

logP, logD, polar

Absorption from small Diffusion rate, membrane
surface area, hydrogen
intestine partition coefficient
bond counts, MWt

Blood protein Binding affinity to blood Plasma protein binding,

binding proteins e.g. albumin logP and logD

Distribution of Binding affinity to cellular

logP, acid or base
compound in tissues membranes
 Ionisation
Ionisation = protonation or deprotonation resulting in charged
molecules
About 85% of marketed drugs contain functional groups that are
ionised to some extent at physiological pH (pH 1.5 8).

The acidity or basicity of a compound plays a major role in controlling:

Absorption and transport to site of action

Solubility, bioavailability, absorption and cell penetration, plasma
binding, volume of distribution
Binding of a compound at its site of action
un-ionised form involved in hydrogen bonding
ionised form influences strength of salt bridges or H-bonds
Elimination of compound
Biliary and renal excretion
CYP P450 metabolism
 How does pH vary in the body?
Fluid pH So the same compound will
Aqueous humour 7.2 be ionised to different extents
Blood 7.4 in different parts of the body.
Colon 5-8
Duodenum (fasting) 4.4-6.6 This means that, for example,
Duodenum (fed) 5.2-6.2 basic compounds will not be
Saliva 6.4 so well absorbed in the
stomach than acidic
Small intestine 6.5
compounds since it is
Stomach (fasting) 1.4-2.1
generally the unionised form
Stomach (fed) 3-7 of the drug which diffuses into
Sweat 5.4 the blood stream.
Urine 5.5-7.0
 Ionisation constants
The equilibrium between un-ionised and ionised forms
is defined by the acidity constant Ka or pKa = -log10 Ka
For an Ka +
acid: HA H + A

[H+][A-] 100
Ka = % ionised =
[AH] 1 + 10(pKa - pH)

For a
Ka +
base: BH+ H + B

[H+][B] 100
Ka = % ionised =
[BH+] 1 + 10(pH - pKa)

When an acid or base is 50% ionised:

pH = pKa
 Ionisation of an acid 2,4-dinitrophenol

100
OH O
90
NO2 NO2
80 -H+
70

60
percent

% neutral
50 NO2 NO2
% anion
40

30 pKa = 4.1
20

10

0
3 4 5 6 7 8 9 10 11
pH
 Ionisation of an base 4-aminopyridine
NH2 NH2

100 -H+
90 +
80
N N
70 H
60
pKa = 9.1
percent

% neutral
50
% cation
40

30

20

10

0
3 4 5 6 7 8 9 10 11
pH
Effect of ionisation on antibacterial potency
of sulphonamides
6.5

6
From pH 11 to 7
5.5 potency increases
5 since active species
is the anion.
potency

4.5

4
From pH 7 to 3
3.5 potency decreases
3 since only the neutral
form of the
2.5
compound can
2 transport into the cell.
2 3 4 5 6 7 8 9 10 11

O O pKa
O O
S R2 S R2
R1 N R1 N
H
-
 Effects of substituents on ionisation
Substituents have similar effects on the ionisation of different series of
compounds.
This is an
5 example of a
linear free energy
log(KX/KH) pyridines

4 3-CN 3-NO2 relationship.

N
3 Trends such as this
are found for a very
X 3-F
2 3-Cl wide range of
aromatic ionising
1 4-F 4-Cl functionalities. This
allows prediction of
H
0 the pKa of molecules
-0.3 -0.2 -0.1 0 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8
log(KX/KH) benzoic acids O OH
before they are even
3-Me
-1 made!
4-Me

X
 Lipophilicity

Lipophilicity (fat-liking) is the most important physical property of a drug

in relation to its absorption, distribution, potency, and elimination.

Lipophilicity is often an important factor in all of the following, which

include both biological and physicochemical properties:

Solubility Biliary and renal clearance

Absorption CNS penetration
Plasma protein binding Storage in tissues
Metabolic clearance Bioavailability
Volume of distribution Toxicity
Enzyme / receptor binding
 The hydrophobic effect
Molecular interactions why dont oil and water mix?
H

H O O H H
H H H
H O H H
H O H O O H H

H H H H
H H
H
O O O H O H H
H H
H H H H H
O O
H O H
H H H H H H
O

This is entropy driven (remember G = H TS). Hydrophobic

molecules are encouraged to associate with each other in water.
Placing a non-polar surface into water disturbs network of water-water
hydrogen bonds. This causes a reorientation of the network of hydrogen
bonds to give fewer, but stronger, water-water H-bonds close to the non-
polar surface.
Water molecules close to a non-polar surface consequently exhibit
much greater orientational ordering and hence lower entropy than bulk
water.
 The hydrophobic effect
This principle also applies to the physical properties of drug molecules.

If a compound is too lipophilic, it may

be insoluble in aqueous media (e.g. gastrointestinal fluid or blood)
bind too strongly to plasma proteins and therefore the free blood
concentration will be too low to produce the desired effect
distribute into lipid bilayers and be unable to reach the inside of the cell

Conversely, if the compound is too polar, it may not be absorbed through

the gut wall due to lack of membrane solubility.

So it is important that the lipophilicity of a potential drug molecule is correct.

How can we measure this?

 Partition coefficients
P
Xaqueous Xoctanol

Partition coefficient P (usually expressed as log10P or logP) is defined as:

[X]octanol
P=
[X]aqueous

P is a measure of the relative affinity of a molecule for the lipid and aqueous
phases in the absence of ionisation.

1-Octanol is the most frequently used lipid phase in pharmaceutical

research. This is because:

It has a polar and non polar region (like a membrane phospholipid)

Po/w is fairly easy to measure
Po/w often correlates well with many biological properties
It can be predicted fairly accurately using computational models
 Calculation of logP
LogP for a molecule can be calculated from a sum of fragmental
or atom-based terms plus various corrections.
logP = S fragments + S corrections
H
C H
Branch H C C clogP for windows output
O
C H C: 3.16 M: 3.16 PHENYLBUTAZONE
H C
H C C Class | Type | Log(P) Contribution Description Value
N
H C C H H
H N FRAGMENT | # 1 | 3,5-pyrazolidinedione -3.240
C H C C
H C H C H
ISOLATING |CARBON| 5 Aliphatic isolating carbon(s) 0.975
H C H
C ISOLATING |CARBON| 12 Aromatic isolating carbon(s) 1.560
O
C EXFRAGMENT|BRANCH| 1 chain and 0 cluster branch(es) -0.130
H H C
C EXFRAGMENT|HYDROG| 20 H(s) on isolating carbons 4.540
H
Phenylbutazone H
EXFRAGMENT|BONDS | 3 chain and 2 alicyclic (net) -0.540

RESULT | 2.11 |All fragments measured clogP 3.165

 Blood clot preventing activity
of salicylic acids
O OH
9
OH

8.5
R1 R2
8
pIC50

7.5 O OH

7 O

O
6.5
2 3 4 5 6 Aspirin
logP
 What else does logP affect?

Binding to Aqueous Binding to Absorption Binding to Binding to

logP enzyme / solubility P450 through blood / tissue hERG heart
receptor metabolising membrane proteins ion channel -
enzymes less drug free cardiotoxicity
to act risk

So log P needs to be optimised

 Distribution coefficients
If a compound can ionise then the observed partitioning between water and
octanol will be pH dependent.

[un-ionised]octanol insignificant
octanol phase
P
Distribution
coefficient D (usually
aqueous phase Ka expressed as logD)
[un-ionised]aq [ionised]aq
is the effective
lipophilicity of a
For an acidic compound: HAaq H+aq+ A-aq compound at a given
pH, and is a function
[HA]octanol of both the
D=
[HA]aq + [A-]aq lipophilicity of the
un-ionised
For a basic compound: BH+aq H+aq+ Baq compound and the
degree of ionisation.
[B]octanol
D=
[BH+]aq + [B]aq
Relationship between logD, logP and pH for
an acidic drug
O
logP=4.25 O
5 OH

4 50% neutral
N
10%
3 O

1%
2
logD

0.1% Cl
1
Indomethacin
0.01%
0
0.001% neutral
-1

-2
2 3 4 5 6 7 8 9 10
pH
For singly ionising acids in general:
pKa=4.50
logD = logP - log[1 + 10(pH-pKa)]
 pH - Distribution behaviour of bases
Cl O
O
4
O O

3 N
H
Amlodipine
O
Cl
O
O pKa=9.3
2
O O NH2

N
1 H
O
logD

H CN
0 NH3+ N N

S
-1 N N N
H H

-2 H CN Cimetidine
N N
pKa=6.8
-3 S
NH+ N N
H H
-4
3 4 5 6 7 8 9 10 11
pH

For singly ionising bases in general:

logD = logP - log[1 + 10(pKa-pH)]
pH - Distribution behaviour of amphoteric
compounds
OH

pKa1 = 4.4 pKa2 = 9.8

0.5
NH2
0

-0.5
logD

-1 O
OH
-1.5

-2 NH2
NH3+
-2.5
2 3 4 5 6 7 8 9 10 11 12
pH
 How can lipophilicity be altered?
R1
O
O N

e.g. Monocarboxylate transporter 1 blockers N

R2

O N S Ar

OH OH OH OH OH OH
R1
N N N N N N N
R2 O O
OH
F

O CF3

X
Ar
N N N N

logD 1.7 2.0 1.2 2.9 2.2 3.2

 How can lipophilicity be altered?
R1
O
O N

e.g. Monocarboxylate transporter 1 blockers N

R2

O N S Ar

OH OH OH OH OH OH
R1
N N N N N N N
R2 O O
OH
F

O CF3

X
Ar
N N N N

logD 1.7 2.0 1.2 2.9 2.2 3.2

 Hydrogen bonding
Intermolecular hydrogen bonds are virtually non-existent between small
molecules in water. To form a hydrogen bond between a donor and
acceptor group, both the donor and the acceptor must first break their
hydrogen bonds to surrounding water molecules
A H OH2 + B HOH A H B + HOH OH2

The position of this equilibrium depends on the relative energies of the

species on either side, and not just the energy of the donor-acceptor
complex
Intramolecular hydrogen bonds are more readily formed in water - they are
entropically more favourable.
O O O
+ +
O H -H O -H O
O - H
O
pKa1=1.91 O pKa2=6.33
OH O O

HO2C + HO2C + CO2-

-H -H

CO2H pKa1=3.03 CO2- pKa2=4.54 CO2-

 Hydrogen bonding and bioavailability
Remember! Most oral drugs are absorbed through the gut wall by
transcellular absorption.
H
H
H O O
O H
H H O
O H O
O
H O H H N H
N H O
O H H
O H + H H N N
H N N
O
O H H O H O H
O H H
H H H H
O O O
H H H
H

De-solvation and formation of a neutral molecule is unfavourable if the

compound forms many hydrogen or ionic bonds with water.
So, as a good rule of thumb, you dont want too many hydrogen bond
donors or acceptors, otherwise the drug wont get from the gut into the
blood.
There are some exceptions to this sugars, for example, but these
have special transport mechanisms.
 Molecular size

Molecular size is one of the most important factors affecting

biological activity, but its also one of the most difficult to
measure.

There are various ways of investigating the molecular size,

including measurement of:

Molecular weight (most important)

Electron density
Polar surface area
Van der Waals surface
Molar refractivity
 25 Molecular weight

20

15
Plot of frequency of
frequency %

occurrence against molecular

weight for 594 marketed oral
10 drugs

0
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
-15 -20 -25 -30 -35 -40 -45 -50 -55 -60 -65 -70 -75 -80 -85 -90 -95 100
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0-
10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95
Molecular Weight

Most oral drugs have molecular weight < 500

 Number of rotatable bonds
A rotatable bond is defined as any single non-ring bond,
attached to a non-terminal, non-hydrogen atom. Amide C-N
bonds are not counted because of their high barrier to rotation.
No. of rotatable
OH
O
H
N bonds
O
Atenolol
H2N

OH
H
O N
Propranolol
 Number of rotatable bonds
A rotatable bond is defined as any single non-ring bond,
attached to a non-terminal, non-hydrogen atom. Amide C-N
bonds are not counted because of their high barrier to rotation.
No. of rotatable Bioavailability
OH
O
H
N bonds
O
Atenolol 8 50%
H2N

OH
H
O N
Propranolol 6 90%

The number of rotatable bonds influences, in particular,

bioavailability and binding potency. Why should this be so?
 Number of rotatable bonds
Remember G = H TS ! A molecule will have to adopt a fixed
conformation to bind, and to pass through a membrane. This involves a
loss in entropy, so if the molecule is more rigid to start with, less entropy
is lost. But beware!
H H H H H H
R R H H R

H H H R R H

Any, or none, of these could be the active conformation!

70
60
50
Percentage of 40
compounds MW 0-499
with F >20% 30 MW 500+
20
10
0
# Rot 0-7 # Rot 8-10 # Rot 11+
 Bulk physical properties

When a compound is nearing nomination for entry

to clinical trials, we need to look at:
Solubility, including in human intestinal fluid
Hygroscopicity, i.e. how readily a compound
absorbs water from the atmosphere
Crystalline forms may have different properties
Chemical stability (not a physical property! Look
at stability to pH, temperature, water, air, etc)

How can these be altered?

Different counter ion or salt

Different method of crystallisation
 This seems like a lot to remember!
There are various guidelines to help, the most well-
known of which is the Lipinski Rule of Five

molecular weight < 500

logP < 5
< 5 H-bond donors (sum of NH and OH)
< 10 H-bond acceptors (sum of N and O)

An additional rule was proposed by Veber

< 10 rotatable bonds

Otherwise absorption and bioavailability are likely to

be poor. NB This is for oral drugs only.
 The Drug Design Conundrum
The conundrum is that while pharmacokinetic properties improve by
modulating bulk properties, potency also depends on these particularly
lipophilicity. There are then three approaches that could be adopted.

Potency
New receptor interaction
to increase potency and modulate
bulk properties

Find a substitution position not affecting

potency where bulk properties can be
modulated for good DMPK

Trade potency for

DMPK improvements
dose to man focus

logD/Clearance/CYP inhibition