Enzyme as Drug Target Lecture Notes PDF

Lecture (2a) Enzyme as drug target Eman Adel Mostafa Saleh Abdulateef Al-Qahtani, PhD Mohammad Alrofaidi, PhD Associate professor of Assistant professor Assistant professor Medicinal Chemistry...

Lecture (2a) Enzyme as drug target Eman Adel Mostafa Saleh Abdulateef Al-Qahtani, PhD Mohammad Alrofaidi, PhD Associate professor of Assistant professor Assistant professor Medicinal Chemistry 1  Course Content Intro to medicinal chemistry Pharmacodynamic and drug target Physiochemical properties in relation to biology and drug target Pharmacokinetics and drug metabolism Cholinergics and anticholinesterase Sympathomimetic agent Aug 2022 Sympatholytic agents 2  Enzyme as drug target 1. Structure and function of enzymes 2. The Active site 3. Substrate Binding 4. Catalysis mechanisms 5. Regulation of Enzymes 6. Overall Process of Enzyme Catalysis 7. Types of enzyme inhibitors a. Reversible inhibitors b. Irreversible inhibitors c. Allosteric inhibitors d. Transition state inhibitors 8. Enzyme targets for useful medications Sep 2022 3 1- Structure and function of enzyme ❑ Enzyme always has the suffix “ase” ❑ Globular proteins (enzymes) acting as the body’s catalysts ❑ Speed up time for reaction to reach equilibrium ❑ Lower the activation energy of a reaction Example: O HO H O LDH O C C NADH + H3C C H3C C + NAD+ OH OH Pyruvic acid Lactic acid LDH = Lactate dehydrogenase (enzyme) NADH = Nicotinamide adenosine dinucleotide (reducing agent & cofactor) Pyruvic acid = Substrate Sep 2022 4 1- Structure and function of enzyme Energy Energy Transition state New transition state Act. Act. energy energy Starting Starting ∆G material ∆G material Product Product WITHOUT ENZYME WITH ENZYME Enzymes lower the activation energy of a reaction but ∆G remains the same ∆G: difference in Gibbs free energy Sep 2022 5 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) ❑ - participate in the enzyme-catalysed reaction Active site Active site ENZYME Sep 2022 6 2- The active site: Example: Sep 2022 7 3- Substrate binding : 3.1 Induced fit Substrate S Induced fit ❖ Active site is nearly the correct shape for the substrate. ❖ Binding alters the shape of the enzyme (induced fit). ❖ The binding process can strain bonds in the substrate. ❖ Binding involves intermolecular bonds between functional groups in the substrate and functional groups in the active site. Sep 2022 8  3- Substrate binding : 3.2 Bonding forces: Example vdw O interaction C O S H3C C H-bond Active site O H ionic Phe Ser O bond CO2 Possible interactions Asp H-Bond van der Waals Ionic Enzyme Sep 2022 9 4- Catalysis mechanisms: 4.1 Acid/base catalysis Histidine +H+ NH NH -H+ N N H Non-ionised Ionised Acts as a basic catalyst Acts as an acid catalyst (proton 'sink') (proton source) 4.2 Nucleophilic residues H H H3N CO2 H3N CO2 L-Serine L-Cysteine OH SH Sep 2022 10 5- Regulation of enzymes: Active site Active site unrecognisable Induced ACTIVE SITE fit (open) Enzyme ENZYME (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 altered and is not recognised by the substrate ❑ Increasing substrate concentration does not reverse inhibition ❑ Inhibitor differs in structure to the substrate Sep 2022 11 * 5- Regulation of enzymes: Biosynthetic pathway S P P’ P’’ P’’’ Enzyme (open) ENZYME Inhibition Feedback control ❑ Enzymes with allosteric sites are often at the start of a biosynthetic pathway ❑ The enzyme is controlled by the final product of the pathway ❑ The final product binds to the allosteric site and switches off the enzyme Sep 2022 12 6- Overall process of enzyme catalysis: S P S P EE E E E E+S ES EP E+P ❑ 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 ❑ Interactions stabilise the transition state ❑ Designing molecules with stronger binding interactions results in enzyme inhibitors which block the active site Sep 2022 13 7- Type of enzyme inhibitors: a. Reversible inhibitors S I I EE E Inhibitor binds reversibly to the active site Intermolecular bonds are involved in binding The inhibitor undergoes no reaction 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 substrate, product or cofactor Sep 2022 14 7- Type of enzyme inhibitors: A. Reversible inhibitors Examples: Diuretics Kinase inhibitors ACE inhibitors Sulfonamides Some Antidepressants Statin Protease inhibitors Sep 2022 15 7- Type of enzyme inhibitors: B. Irreversible inhibitors X Covalent Bond X OH OH O 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 Sep 2022 16 7- Type of enzyme inhibitors: B. Irreversible inhibitors Examples: o Nerve gas o Penicillins o Cephalosporins o PPI (proton pump inhibitors) o Orlistat Sep 2022 17 Examples - orlistat Orlistat C6H13 C11H23 O O O C11H23 O O C6H13 NHCHO C11H23 O But NHCHO O C6H13 But O O OH O H O O O O But NHCHO Ser Ser Ser Pancreatic lipase Pancreatic lipase Pancreatic lipase Orlistat is an anti-obesity drug that inhibits pancreatic lipase The enzyme is blocked from digesting fats in the intestine Fatty acids and glycerol are less absorbed as a result of this interaction Leads to reduced biosynthesis of fat in the body 18  7- Type of enzyme inhibitors: C. Allosteric inhibitors Active site Active site unrecognisable Induced ACTIVE SITE fit (open) Enzyme ENZYME (open) Enzyme ENZYME Allosteric binding 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 Sep 2022 19 7- Type of enzyme inhibitors: D. Transition state inhibitors Drugs designed to mimic the transition state of an enzyme-catalysed reaction Transition-state inhibitors are potentially bind very strongly to the active site more than substrate or the products. Transition state inhibitor can be describe as thermodynamically stable. E.g: Saquinavir (HIV protease transition state analogue) Sep 2022 20 D. Transition-state Inhibitors: Example: Renin inhibitors Inhibitor Angiotensin converting Renin enzyme (ACE) Angiotensinogen Angiotensin I Angiotensin II ❑ Renin inhibitors block synthesis of angiotensin I and II ❑ Angiotensin II constricts blood vessels and raises blood pressure ❑ Renin inhibitors act as antihypertensives (lower blood pressure) Sep 2022 21 8- Enzyme target for useful medications: A. Antibacterial agents Dihydropteroate synthetase, transpeptidase. B. Antiviral agents HIV reverse transcriptase, HIV protease, viral DNA polymerase C. Anti-inflammatory agents Cyclooxygenase D. Cholesterol lowering agents HMG-CoA reductase E. Antidepressants Monoamine oxidase F. Anticancer agents Tyrosine kinase, dihydrofolate reductase, thymidylate synthase, aromatase. Sep 2022 22 23