Medical Biochemistry
Enzymes and enzyme inhibitors - Hochstenbach
ΔG = Gibbs free energy of products minus Gibbs free energy of reactants > provides no information of
rate of reaction
When ΔG<0 a reaction can occur spontaneously and releases Gibbs free energy > exergonic reaction
When ΔG>0, an input of Gibbs free energy is required > endergonic reaction
Enzymes accelerate reactions by facilitating formation of transition state (lowering the activation
energy)
Prosthetic group = cofactor that is tightly or even covalently bound to enzyme
Enzyme classes:
- Oxido-reductase: one molecule is oxidized while another is reduced > oxidase, oxygenase,
dehydrogenase, reductase
- Transferase: transfers a group > e.g. kinase (transfers phosphate groups)
- Hydrolase: hydrolysis, wherein a group is split of > e.g. protease, nuclease, phosphatase, ATPase
- Lyase (synthase): a group is removed, wherein often a double bond or ring structure is formed >
e.g. carboxylase, adenylate cyclase
- Isomerase: a group is moved to another place in the same molecule
- Ligase (synthetase): two substrates are ligated, at the cost of ATP hydrolysis
Parameters in enzyme kinetics:
- Vmax = maximum rate of enzyme activity
- Km = Michaelis constant = the substrate concentration at which the reaction rate is half its
maximum value (1/2 Vmax) > the lower the Km, the higher the affinity of the substrate to the
enzyme’s substrate binding site
- Kcat = turnover number = the number of substrate molecules converted into product by an
enzyme molecule in a unit time when the enzyme is fully saturated with substrate
Enzyme inhibitors:
- That bound reversibly (through hydrogen bond/vanderwaals interaction)
Competitive inhibitors (substrate and inhibitor bind to same substrate binding site) >
Increased apparent Km, but Vmax unchanged
, Ibuprofen, statins, Bortezomib, oseltamivir (Tamiflu)
Non-competitive inhibitors (inhibitor binds at allosteric site=other than active site) > Km
unchanged, but decreased apparent Vmax
- That bound irreversibly > decreased Vmax, because fewer active enzymes
(‘Normal’) irreversible inhibitors
Aspirin
Mechanism based (‘suicide’) inhibitors
Penicillin
Allosteric inhibiting can refer to:
- Non-competitive inhibition > inhibitor binds to allosteric site and substrate can still bind, but
enzyme cannot catalyze reaction
- Competitive inhibition > inhibitor binds to allosteric site and substrate cannot bind anymore
All noncompetitive inhibitors are allosteric inhibitors, but not all allosteric inhibitors are
noncompetitive inhibitors
Suicide inhibitors:
- Modified substrates that modify the active site of an enzyme
- First they bind reversibly (like a normal substrate) > the catalytic mechanism of the enzyme
generates a reactive intermediary that binds covalently (irreversibly) to the enzyme and in that
way inactivates it
- The enzyme ‘commits suicide’ by modifying the inhibitor
- For example MAO
Cytochrome P450 enzymes (CYP)
- Proteins that transfers electrons, using heme as its prosthetic group
- The iron of a cytochrome alternates between a oxidized (Fe3+) and reduced (Fe2+) state during
electron transport
- Coenzyme: NADPH
- (Cytochrome P450 (CYP) is a family of cytochromes that absorbs light maximally at 450 nm when
complexed in vitro with exogenous carbon monoxide)
- 57 different human CYP-enzymes, can be divided into 2 groups:
Those that metabolize xenobiotic (foreign) molecules (e.g. drugs, pollutants,
agrochemicals)
Those that participate in key biosynthetic pathways (e.g. biosynthesis of sterols and
vitamin D)
Drug development - Hochstenbach
Two approaches to drug discovery:
Enzymes and enzyme inhibitors - Hochstenbach
ΔG = Gibbs free energy of products minus Gibbs free energy of reactants > provides no information of
rate of reaction
When ΔG<0 a reaction can occur spontaneously and releases Gibbs free energy > exergonic reaction
When ΔG>0, an input of Gibbs free energy is required > endergonic reaction
Enzymes accelerate reactions by facilitating formation of transition state (lowering the activation
energy)
Prosthetic group = cofactor that is tightly or even covalently bound to enzyme
Enzyme classes:
- Oxido-reductase: one molecule is oxidized while another is reduced > oxidase, oxygenase,
dehydrogenase, reductase
- Transferase: transfers a group > e.g. kinase (transfers phosphate groups)
- Hydrolase: hydrolysis, wherein a group is split of > e.g. protease, nuclease, phosphatase, ATPase
- Lyase (synthase): a group is removed, wherein often a double bond or ring structure is formed >
e.g. carboxylase, adenylate cyclase
- Isomerase: a group is moved to another place in the same molecule
- Ligase (synthetase): two substrates are ligated, at the cost of ATP hydrolysis
Parameters in enzyme kinetics:
- Vmax = maximum rate of enzyme activity
- Km = Michaelis constant = the substrate concentration at which the reaction rate is half its
maximum value (1/2 Vmax) > the lower the Km, the higher the affinity of the substrate to the
enzyme’s substrate binding site
- Kcat = turnover number = the number of substrate molecules converted into product by an
enzyme molecule in a unit time when the enzyme is fully saturated with substrate
Enzyme inhibitors:
- That bound reversibly (through hydrogen bond/vanderwaals interaction)
Competitive inhibitors (substrate and inhibitor bind to same substrate binding site) >
Increased apparent Km, but Vmax unchanged
, Ibuprofen, statins, Bortezomib, oseltamivir (Tamiflu)
Non-competitive inhibitors (inhibitor binds at allosteric site=other than active site) > Km
unchanged, but decreased apparent Vmax
- That bound irreversibly > decreased Vmax, because fewer active enzymes
(‘Normal’) irreversible inhibitors
Aspirin
Mechanism based (‘suicide’) inhibitors
Penicillin
Allosteric inhibiting can refer to:
- Non-competitive inhibition > inhibitor binds to allosteric site and substrate can still bind, but
enzyme cannot catalyze reaction
- Competitive inhibition > inhibitor binds to allosteric site and substrate cannot bind anymore
All noncompetitive inhibitors are allosteric inhibitors, but not all allosteric inhibitors are
noncompetitive inhibitors
Suicide inhibitors:
- Modified substrates that modify the active site of an enzyme
- First they bind reversibly (like a normal substrate) > the catalytic mechanism of the enzyme
generates a reactive intermediary that binds covalently (irreversibly) to the enzyme and in that
way inactivates it
- The enzyme ‘commits suicide’ by modifying the inhibitor
- For example MAO
Cytochrome P450 enzymes (CYP)
- Proteins that transfers electrons, using heme as its prosthetic group
- The iron of a cytochrome alternates between a oxidized (Fe3+) and reduced (Fe2+) state during
electron transport
- Coenzyme: NADPH
- (Cytochrome P450 (CYP) is a family of cytochromes that absorbs light maximally at 450 nm when
complexed in vitro with exogenous carbon monoxide)
- 57 different human CYP-enzymes, can be divided into 2 groups:
Those that metabolize xenobiotic (foreign) molecules (e.g. drugs, pollutants,
agrochemicals)
Those that participate in key biosynthetic pathways (e.g. biosynthesis of sterols and
vitamin D)
Drug development - Hochstenbach
Two approaches to drug discovery:
