DRUG TARGETS: ENZYMES

1. Chapter3 DRUG TARGETS: ENZYMES

2. Namingenzymes • 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 • IsomerasesIntramolecular 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. Energy Energy Transition state New transition state Act. energy Act. energy Starting material Starting material ∆G ∆G Product Product WITH ENZYME WITHOUT ENZYME Structure and function of enzymes Lowering the activation energy of reaction 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. Active site Active site 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 ENZYME

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

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

10. Phe Phe S S H O H O Ser Ser CO2 Induced fit CO2 Asp Asp Substrate binding Bonding forces • Induced fit - Active site alters shape to maximise intermolecular • bonding • 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. O O O Substrate binding Example- Binding of pyruvic acid in LDH O H H3N

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

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

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

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

16. : : O C N H P r o t e i n P r o t e i n H : .. N N : O H O O Chymotrypsin S e r H i s A s p Catalysis mechanisms Mechanism for chymotrypsin

17. H : N N : H O O Chymotrypsin S e r H i s A s p Catalysis mechanisms Mechanism for chymotrypsin

18. S e r H i s A s p Catalysis mechanisms Mechanism for chymotrypsin H N : : O O Chymotrypsin

19. S e r H i s A s p Catalysis mechanisms Mechanism for chymotrypsin H : N N : : O O Chymotrypsin

20. S e r H i s A s p Catalysis mechanisms Mechanism for chymotrypsin H : N N : : O O Chymotrypsin

21. S e r H i s A s p Catalysis mechanisms Mechanism for chymotrypsin H N : : O O Chymotrypsin

22. H : .. N N : O H O O Chymotrypsin S e r H i s A s p Catalysis mechanisms Mechanism for chymotrypsin

23. Catalysis mechanisms Mechanism for chymotrypsin

24. E E P S S E + S P E E E ES EP E + P Overall process of enzyme catalysis • 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. Active site unrecognisable Active site Induced fit (open) Enzyme ENZYME Allosteric binding site ACTIVE SITE Allosteric inhibitor (open) Enzyme ENZYME Regulation of enzymes • 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. Biosynthetic pathway S P P’’’ P’ P’’ Feedback control (open) Enzyme ENZYME Regulation of enzymes 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. Phosphorylase b (inactive) Signal cascade Protein kinase Phosphorylase a (active) Glycogen Glucose-1-phosphate Cell 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 kinasesphosphorylate target enzymes to affect activity • Example Adrenaline