1. An Introduction to Medicinal Chemistry 3/e PROTEINS AS DRUG TARGETS:
Patrick
An Introduction to Medicinal Chemistry 3/e
Chapter 4
PROTEINS AS DRUG TARGETS:
ENZYMES

2. Contents
1. Structure and function of enzymes (3 slides) 2. The active site 3. Substrate binding Induced fit Bonding forces (5 slides) 4. Catalysis mechanisms Acid/base catalysis 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]

3. 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:
LDH = Lactate dehydrogenase (enzyme)
NADH2 = Nicotinamide adenosine dinucleotide (reducing agent & cofactor)
Pyruvic acid = Substrate

4. 1. Structure and function of enzymes
Lowering the activation energy of reaction
WITHOUT ENZYME
Product
Starting
material
Energy
WITH ENZYME
Product
Starting
material
Energy
Transition state
New
transition
state
Act.
energy
Act.
energy ∆G ∆G
Enzymes lower the activation energy of a reaction but DG remains the same.

5. 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

6. 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

7. 3. Substrate binding 3.1 Induced fit 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

8. 3. Substrate binding 3.2 Bonding forces Ionic H-bonding van der Waals
Example:
vdw
interaction S
Phe
H-bond
Active site
Ser O H
ionic
bond
Asp
CO2
Enzyme

9. 3. Substrate binding 3.2 Bonding forces Ionic H-bonding van der Waals
Example: Binding of pyruvic acid in LDH
H-Bond O H
H3N
H-Bond
Ionic
van der Waals
Ionic
bond
vdw-interactions
Possible interactions

10. 3. Substrate binding 3.2 Bonding forces
Induced fit - Active site alters shape to maximise intermolecular bonding S
Phe
Ser O H
Asp
CO2 S
Phe
Ser O H
Asp
CO2
Induced
fit
Intermolecular bond lengths optimised
Susceptible bonds in substrate strained
Susceptible bonds in substrate more easily broken
Intermolecular bonds not optimum length for maximum bonding

11. 3. Substrate binding
Example: Binding of pyruvic acid in LDH O H O
H3N

12. 3. Substrate binding Example: Binding of pyruvic acid in LDH pi bond
weakened H
H3N

13. 4. Catalysis mechanisms 4.1 Acid/base catalysis Histidine
Non-ionised
Acts as a basic catalyst
(proton 'sink')
Ionised
Acts as an acid catalyst
(proton source)
4.2 Nucleophilic residues
L-Serine
L-Cysteine

14. 4. Catalysis mechanisms
Serine acting as a nucleophile

15. 5. Overall process of enzyme catalysis
E + P S E ES P E EP
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

16. 6. Competitive (reversible) inhibitors
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

17. 7. Non competitive (irreversible) inhibitorsOH X OH X O
Covalent Bond
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

18. 8. Non competitive (reversible) allosteric inhibitors
(open)
ENZYME
Enzyme
Induced
fit
Active site
unrecognisable
Active site
ACTIVE SITE
(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

19. 8. Non competitive (reversible) allosteric inhibitors
Biosynthetic pathway P S
(open)
ENZYME
Enzyme
Feedback control
Inhibition
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