1. Chapter 3
DRUG TARGETS:
ENZYMES

2. Classification Reaction Type Catalyzed
Naming enzymes
Root + ase
Classification Reaction Type Catalyzed
Oxidoreductases Oxidation Reduction Reactions
Transferases Group transfer Reactions
Hydrolases Hydrolysis Reactions
Lyases Addition or removal of groups to form
double bonds
Isomerases Intramolecular group transfers
Ligases Joining two substrates

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

4. 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. Structure and function of enzymes
Methods of enzyme catalysis
Provides a reaction surface (the active site)
Provides a suitable environment (hydrophobic)
Brings reactants together
Positions reactants correctly for reaction
Weakens bonds in the reactants
Provides acid / base catalysis
Provides nucleophilic groups

6. 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. Substrate binding Induced fit Induced fit
Active site is nearly the correct shape for the substrate
Binding alters the shape of the enzyme (induced fit)
Binding strains bonds in the substrate
Binding involves intermolecular bonds between functional groups in the substrate and functional groups in the active site

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

10. Substrate binding 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 bonds not optimum length for maximum bonding
Intermolecular bond lengths optimised
Susceptible bonds in substrate strained
Susceptible bonds in substrate more easily broken

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

12. Substrate binding Example - Binding of pyruvic acid in LDH p bond
weakened H
H3N

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

14. Catalysis mechanisms Serine acting as a nucleophile H2O Ser O H S e r

15. Catalysis mechanisms
Mechanism for chymotrypsin to hydrolyses peptide bonds
Catalytic triad of serine, histidine and aspartate
Chymotrypsin N O H S e r i s A p .. :

16. Catalysis mechanisms Mechanism for chymotrypsin Chymotrypsin : P r o t.. :

17. Catalysis mechanisms Mechanism for chymotrypsin Chymotrypsin N H O S e:

18. Catalysis mechanisms Mechanism for chymotrypsin Chymotrypsin H N : : O

19. Catalysis mechanisms Mechanism for chymotrypsin Chymotrypsin H : N N :

20. Catalysis mechanisms Mechanism for chymotrypsin Chymotrypsin H : N N :

21. Catalysis mechanisms Mechanism for chymotrypsin Chymotrypsin H N : : O

22. Catalysis mechanisms Mechanism for chymotrypsin Chymotrypsin N O H S e.. :

23. Catalysis mechanisms
Mechanism for chymotrypsin

24. 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
Interactions must be weak enough to allow the product to depart
Implies a fine balance
Designing molecules with stronger binding interactions results in enzyme inhibitors which block the active site

25. Regulation of enzymes
Many enzymes are regulated by agents within the cell
Regulation may enhance or inhibit the enzyme
The products of some enzymes may act as inhibitors
Usually bind to a binding site called an allosteric binding site
Example

26. Regulation of enzymes
(open)
ENZYME
Enzyme
Induced
fit
Active site
unrecognisable
Active site
ACTIVE SITE
(open)
ENZYME
Enzyme
Allosteric
binding site
Allosteric
inhibitor
Inhibitor binds reversibly to an allosteric binding 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

27. Regulation of enzymes
P’’’
P’’ P’
Biosynthetic pathway P S
(open)
ENZYME
Enzyme
Feedback control
Inhibition
Enzymes with allosteric sites are often at the start of a biosynthetic pathway
Enzyme is controlled by the final product of the pathway
Final product binds to the allosteric site and switches off enzyme

28. Regulation of enzymes
External signals can regulate the activity of enzymes (e.g. neurotransmitters or hormones)
Chemical messenger initiates a signal cascade which activates enzymes called protein kinases
Protein kinases phosphorylate target enzymes to affect activity
Example
Protein
kinase
Cell
Phosphorylase b
(inactive)
Phosphorylase a
(active)
Signal
cascade
Adrenaline
Glycogen
Glucose-1-phosphate