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

2. 1 © 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]

3. 1 © 1. Structure and function of enzymes Globular proteins acting as the body’s catalystsGlobular proteins acting as the body’s catalysts Speed up time for reaction to reach equilibriumSpeed up time for reaction to reach equilibrium Lower the activation energy of a reactionLower the activation energy of a reaction Example: LDH = Lactate dehydrogenase (enzyme) NADH = Nicotinamide adenosine dinucleotide (reducing agent & cofactor) Pyruvic acid = Substrate

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

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6. 1 © Methods of enzyme catalysis Provide a reaction surface (the active site)Provide a reaction surface (the active site) Provide a suitable environment (hydrophobic)Provide a suitable environment (hydrophobic) Bring reactants togetherBring reactants together Position reactants correctly for reactionPosition reactants correctly for reaction Weaken bonds in the reactantsWeaken bonds in the reactants Provide acid / base catalysisProvide acid / base catalysis Provide nucleophilesProvide nucleophiles 1. Structure and function of enzymes Link

7. 1 © 2. The active site Hydrophobic hollow or cleft on the enzyme surfaceHydrophobic hollow or cleft on the enzyme surface Accepts reactants (substrates and cofactors)Accepts reactants (substrates and cofactors) Contains amino acids whichContains amino acids which - bind reactants (substrates and cofactors) - bind reactants (substrates and cofactors) - catalyse the reaction - catalyse the reaction ENZYME Active site

8. 1 © Substrate Binding

9. 1 © 3. Substrate binding Active site is nearly the correct shape for the substrateActive site is nearly the correct shape for the substrate Binding alters the shape of the enzyme (induced fit)Binding alters the shape of the enzyme (induced fit) Binding will strain bonds in the substrateBinding will strain bonds in the substrate Binding involves intermolecular bonds between functional groups in the substrate and functional groups in the active siteBinding involves intermolecular bonds between functional groups in the substrate and functional groups in the active site 3.1 Induced fit Induced fit Substrate S

10. 1 © Forces Involved in Binding

11. 1 © IonicIonic H-bondingH-bonding van der Waalsvan der Waals 3.2 Bonding forces Example: S Enzyme Active site vdwinteraction ionicbond H-bond Phe Ser O H Asp CO 2 3. Substrate binding

12. 1 © van der Waals H-Bond Ionic IonicIonic H-bondingH-bonding van der Waalsvan der Waals 3.2 Bonding forces Example: Binding of pyruvic acid in LDH O H H3NH3N H-Bond Ionic bond Possible interactions vdw-interactions 3. Substrate binding

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14. 1 © Induced fit - Active site alters shape to maximise intermolecular bondingInduced fit - Active site alters shape to maximise intermolecular bonding 3.2 Bonding forces Intermolecular bonds not optimum length for maximum bonding Intermolecular bond lengths optimised Susceptible bonds in substrate strained Susceptible bonds in substrate more easily broken S Phe Ser O H Asp CO 2 Induced fit S Phe Ser O H Asp CO 2 3. Substrate binding Link

15. 1 © Example: Binding of pyruvic acid in LDH O H H3NH3N O O O 3. Substrate binding

16. 1 © Example: Binding of pyruvic acid in LDH O H H3NH3N pi bond weakened 3. Substrate binding

17. 1 © 4. Catalysis mechanisms HistidineHistidine 4.1 Acid/base catalysis 4.2 Nucleophilic residues Non-ionised Acts as a basic catalyst (proton 'sink') Ionised Acts as an acid catalyst (proton source) L-SerineL-Cysteine

18. 1 © Catalytic Mechanisms: Serine Acting as a Nucleophile Link Serine side chain

19. 1 © 5. Overall process of enzyme catalysis S E ES P E EP P E E + P E S E + S E Binding interactions must be;Binding interactions must be; - strong enough to hold the substrate sufficiently long for the reaction to occur - strong enough to hold the substrate sufficiently long for the reaction to occur - weak enough to allow the product to depart - weak enough to allow the product to depart Implies a fine balanceImplies a fine balance Drug design - designing molecules with stronger binding interactions results in enzyme inhibitors which block the active siteDrug design - designing molecules with stronger binding interactions results in enzyme inhibitors which block the active site

20. 1 © Competitive Inhibitors

21. 1 © 6. Competitive (reversible) inhibitors Inhibitor binds reversibly to the active siteInhibitor binds reversibly to the active site Intermolecular bonds are involved in bindingIntermolecular bonds are involved in binding No reaction takes place on the inhibitorNo reaction takes place on the inhibitor Inhibition depends on the strength of inhibitor binding and inhibitor concentrationInhibition depends on the strength of inhibitor binding and inhibitor concentration Substrate is blocked from the active siteSubstrate is blocked from the active site Increasing substrate concentration reverses inhibitionIncreasing substrate concentration reverses inhibition Inhibitor likely to be similar in structure to the substrateInhibitor likely to be similar in structure to the substrate I EE S I E

22. 1 © Irreversible Inhibitors

23. 1 © 7. Non competitive (irreversible) inhibitors Inhibitor binds irreversibly to the active siteInhibitor binds irreversibly to the active site Covalent bond formed between the drug and the enzymeCovalent bond formed between the drug and the enzyme Substrate is blocked from the active siteSubstrate is blocked from the active site Increasing substrate concentration does not reverse inhibitionIncreasing substrate concentration does not reverse inhibition Inhibitor likely to be similar in structure to the substrateInhibitor likely to be similar in structure to the substrate X OH X O Covalent Bond Irreversible inhibition

24. 1 © ACTIVE SITE (open) ENZYME Enzyme 8. Non competitive (reversible) allosteric inhibitors Inhibitor binds reversibly to the allosteric siteInhibitor binds reversibly to the allosteric site Intermolecular bonds are formedIntermolecular bonds are formed Induced fit alters the shape of the enzymeInduced fit alters the shape of the enzyme Active site is distorted and is not recognised by the substrateActive site is distorted and is not recognised by the substrate Increasing substrate concentration does not reverse inhibitionIncreasing substrate concentration does not reverse inhibition Inhibitor is not similar in structure to the substrateInhibitor is not similar in structure to the substrate Allostericsite Active site (open) ENZYME Enzyme Induced fit Active site unrecognisable Allosteric inhibitor

25. 1 © 8. Non competitive (reversible) allosteric inhibitors Enzymes with allosteric sites often at start of biosynthetic pathwaysEnzymes with allosteric sites often at start of biosynthetic pathways Enzyme is controlled by the final product of the pathwayEnzyme is controlled by the final product of the pathway Final product binds to the allosteric site and switches off enzymeFinal product binds to the allosteric site and switches off enzyme Inhibitor may have a similar structure to the final productInhibitor may have a similar structure to the final product P’’’ P’’P’ Biosynthetic pathway Feedback control Inhibition PS (open) ENZYME Enzyme Link