Chapter 3 DRUG TARGETS: ENZYMES

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

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

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

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

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

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

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

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

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

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

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

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

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

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 .. :

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

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

Catalysis mechanisms Mechanism for chymotrypsin Chymotrypsin H N : : O

Catalysis mechanisms Mechanism for chymotrypsin Chymotrypsin H : N N :

Catalysis mechanisms Mechanism for chymotrypsin Chymotrypsin H : N N :

Catalysis mechanisms Mechanism for chymotrypsin Chymotrypsin H N : : O

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

Catalysis mechanisms Mechanism for chymotrypsin

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

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

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

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

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