Patrick

An Introduction to Medicinal Chemistry 3/e

Chapter 4

PROTEINS AS DRUG
TARGETS:
ENZYMES
Contents
1. Structure and function of enzymes (3 slides)
2. The active site
3. Substrate binding
3.1. Induced fit
3.2. Bonding forces (5 slides)
4. Catalysis mechanisms
4.1. Acid/base catalysis
4.2. Nucleophilic residues
5. Overall process of enzyme catalysis
6. Competitive (reversible) inhibitors
7. Non competitive (irreversible) inhibitors
8. Non competitive (reversible) allosteric inhibitors (2 slides)

[18 slides]
 1. Structure and function of enzymes

• Globular proteins acting as the body’s catalysts

• Speed up time for reaction to reach equilibrium
• Lower the activation energy of a reaction by stabilizing the
transition state
Example:
O HO H
O LDH O
C C
NADH2 + H3C C H3C C + NAD+
OH OH
Pyruvic acid Lactic acid

LDH = Lactate dehydrogenase (enzyme)

NADH2 = Nicotinamide adenosine dinucleotide (reducing agent & cofactor)
Pyruvic acid = Substrate
 1. Structure and function of enzymes

Lowering the activation energy of reaction

Energy Energy
Transition state
New
transition
Act. state
energy Act.
energy
Starting Starting
∆G ∆G
material material

Product Product

WITHOUT ENZYME WITH ENZYME

• Enzymes lower the activation energy of a reaction but G

remains the same.
 1. Structure and function of enzymes
Methods of enzyme catalysis

• Provide a reaction surface (the active site)

• Provide a suitable environment (hydrophobic)
• Bring reactants together
• Position reactants correctly for reaction
• Weaken bonds in the reactants
• Provide acid / base catalysis
• Provide nucleophiles
 2. The active site
• Hydrophobic hollow or cleft on the enzyme surface
• Accepts reactants (substrates and cofactors)
• Contains amino acids which
- bind reactants (substrates and cofactors)
- catalyse the reaction

Active site
Active site

ENZYME
 3. Substrate binding
3.1 Induced fit

Substrate
S

Induced fit

• Active site is nearly the correct shape for the substrate

• Binding alters the shape of the enzyme (induced fit)
• Binding will strain bonds in the substrate
• Binding involves intermolecular bonds between functional
groups in the substrate and functional groups in the active site
3. Substrate binding
3.2 Bonding forces
• Ionic
• H-bonding
• van der Waals

Example: vdw
interaction

S
H-bond
Active site
H ionic
O Phe
bond
Ser
CO2

Asp

Enzyme
3. Substrate binding
3.2 Bonding forces
• Ionic
• H-bonding
• van der Waals

Example: Binding of pyruvic acid in LDH

O O
H-Bond H
C O
H3C C O
Ionic
C O bond
O H3C C
H3N
O
Possible interactions vdw-interactions

H-Bond
van der Waals
Ionic
 3. Substrate binding
3.2 Bonding forces
• Induced fit - Active site alters shape to maximise
intermolecular bonding

Phe
Phe
S S
H
O
H
O Ser
Ser CO2
CO2 Induced
Asp fit Asp

Intermolecular bonds not Intermolecular bond lengths optimised

optimum length for Susceptible bonds in substrate strained
maximum bonding Susceptible bonds in substrate more
easily broken
3. Substrate binding
Example: Binding of pyruvic acid in LDH

C O
H3C C
H3N
O
3. Substrate binding
Example: Binding of pyruvic acid in LDH

O
pi bond H
weakened
O

C O
H3C C
H3N
O
 4. Catalysis mechanisms
4.1 Acid/base catalysis
• Histidine +H
NH NH
N -H N
H
Non-ionised Ionised
Acts as a basic catalyst Acts as an acid catalyst
(proton 'sink') (proton source)

4.2 Nucleophilic residues

H H
H3N CO2 H3N CO2

L-Serine L-Cysteine
OH SH
 4. Catalysis mechanisms

Serine acting as a nucleophile

Substrate

H2O
HO Product

OH O OH

Ser Ser Ser

 5. Overall process of enzyme catalysis

S P
S P

EE E E E

E+S ES EP E+P

• Binding interactions must be;

- strong enough to hold the substrate sufficiently long for the
reaction to occur
- weak enough to allow the product to depart
• Implies a fine balance
• Drug design - designing molecules with stronger binding
interactions results in enzyme inhibitors which block the active
site
 6. Competitive (reversible) inhibitors

S
I

EE E

• Inhibitor binds reversibly to the active site

• Intermolecular bonds are involved in binding
• No reaction takes place on the inhibitor
• Inhibition depends on the strength of inhibitor binding and
inhibitor concentration
• Substrate is blocked from the active site
• Increasing substrate concentration reverses inhibition
• Inhibitor likely to be similar in structure to the substrate
 7. Non competitive (irreversible) inhibitors
X

Covalent Bond

OH OH O

Irreversible inhibition

• Inhibitor binds irreversibly to the active site

• Covalent bond formed between the drug and the enzyme
• Substrate is blocked from the active site
• Increasing substrate concentration does not reverse inhibition
• Inhibitor likely to be similar in structure to the substrate
 8. Non competitive (reversible) allosteric inhibitors
Active site
Active site
unrecognisable

Induced
ACTIVE SITE
fit
(open)
Enzyme
ENZYME
(open)
Enzyme
ENZYME
Allosteric
site

Allosteric
inhibitor

• Inhibitor binds reversibly to the allosteric site

• Intermolecular bonds are formed
• Induced fit alters the shape of the enzyme
• Active site is distorted and is not recognised by the substrate
• Increasing substrate concentration does not reverse inhibition
• Inhibitor is not similar in structure to the substrate
 8. Non competitive (reversible) allosteric inhibitors

Biosynthetic pathway

S P P’ P’’ P’’’

Enzyme
(open)
ENZYME

Inhibition Feedback control

• Enzymes with allosteric sites often at start of biosynthetic

pathways
• Enzyme is controlled by the final product of the pathway
• Final product binds to the allosteric site and switches off
enzyme
• Inhibitor may have a similar structure to the final product