Introduction
 Enzymes are soluble proteins, floating in interstitial or
extrastetial fluids. For example, in cell cytosol and in
blood.
 Enzyme catalyses a chemical reaction on the substrate
structure.
 Substrate will inter enzyme active site then converted
into metabolite
 Ligand binds to receptor to activate, then leave
without any change in its structure
Enzyme activates reaction by:
 Lowering transition state and intermediate energy
level.
 Raising the ground state energy of substrate….this
means substrate will be energetically unstable
Enzyme Active site
 Substrate binds to small area in enzyme structure
known as active site:
 Other names: Binding site, Binding domain, Active
pocket
Enzyme Active site
 Two types of amino acids available inside enzyme acite
site:
 Catalytic amino acids: directly or indirectly participate
in enzyme-substrate interactions
 Non-catalytic amino acids:


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Complete the construction of active site pocket
Help shaping tunnels and opening to active site, especially
when the pocket is deep inside.
Might play role in binding (anchoring) substrate to bring it
close to catalytic amino acids
Enzyme Catalysis
 Is characterized by:
 Specificity
 Rate acceleration
 Reaction specificity: can be classified as:
 Reaction specificity
 Substrate specificity
 Rate acceleration is due to the presence of Co-enzymes
in most of the cases
Co-Enzymes
 Are any organic molecules or metal ions that are
essential for catalytic action of enzyme.
 Examples:
 ATP
 Coenzyme A
 Glutathione
 Ascorbic acid
 Lipoic acid
 Zn, Co, Fe, Mg cations
 ATP exists in the active site of ATP-dependent
phosphofructokinase
Substrate specificity
 Substrate specificity can be categorized into:
 Very specific: one type of substrate can fit the active site
Examples: carboxyesterase, COMT, Acetylcholinesterase
 Broad: more than one substrate can bind and converted
into metabolite. Cytochrome P450 is an example
 Enzymes are substrate specific because:
 They have distinguished active site compared to others
 Different amino acids in active site play a major role in
specificity.
Binding specificity
 Sub-levels of Substrate specificity are:
 Regio-specificity: here the enzyme will catalyze its
reaction on specific group at specific position although
other identical group is available elsewhere

Example: COMT will methylate hydroxy group that is meta to
amino ethylene group
Binding specificity
 Determinant factors that make enzymes Regio-
specific:
 Which group is the closest to the catalytic amino acids
 Which group is the nearest to the site where Co-enzyme
lies:



ATP for phosphorylation
NADH/NAD+ for redox reaction
SAM for methylation
 Substrate in yellow and NADH in Red
Binding specificity
 Sub-levels of Substrate specificity are:
 Stereo-specificity: here the enzyme will catalyze its
reaction on one of substrate isomers or enantiomer
more than the other
 This is why some drug will be active only when they are
in its pure S or R isomer form
 Examples:



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R isomer of Adrenaline is much more active than S
R isomer of Salbutamol is much more active than S
S-methacoline is more active than R-methacoline
S-ibuprofen is more active than R-ibuprofen
Why is Enzyme specific?
 Because enzyme is chiral molecule, only L-amino acids
are available and amino acids are all chiral except
Glycine (Why)
 Chiral compounds will bind to form diastereomers (E-S
complex), that have different physicochemical
properties…. The most stable diastereomer will be
energetically favored to form.
 Also amino acid residues available in active site might
play a role in this specificity
Because of that Enzyme will bind preferentially to one
isomer more than the other to form the more stable E-S complex
Enzyme also can differentiate
between identical proton:
 Even if substrate is
achiral, enzyme can
distinguish between
identical hydrogen
atoms. Why?
 Since two pockets are
specific for R1 and R2,
this will push one of the
identical proton to be
close to basic nitrogen
to be removed.
Rate acceleration
 Enzyme accelerate reactions by:
 Stabilizing the reaction transition state…. This will lower
the activation energy.
 By destabilizing drug molecule
 Bring drug close to the cofactor that normally carries
reactive species such as phosphate, hydride, oxygen, …
 Reaction rate could reach 1010 – 1014 the rate of non-
enzymatic reactions
Enzyme turnover
 Is the number of molecules of substrate converted to
product per unit time per molecule of enzyme active
site
 Some enzyme have multiple subunits and each
subunit might have more than one active site.
 As the number of subunits increased, turnover
number increased
Classification of amino acids
Enzyme inhibition
 Enzyme inhibitor: will slow down or block enzyme
catalysis
 Mainly irreversible ……. Enzyme inactivation
 The consequences of enzyme inhibition depends on
the function of the enzyme
 Examples:
 GABA aminotransferase deactivates GABA…. Inhibition
of this enzyme will accumulate GABA ….Anticonvulsant
action
 Xanthine will be oxidized into uric acid…. Inhibition of
this enzyme will help in Gout patients
Enzyme inhibition
 Enzyme inhibitor: will slow down or block enzyme
catalysis
 Mainly irreversible ……. Enzyme inactivation
 The consequences of enzyme inhibition depends on
the function of the enzyme
 Examples:
 GABA aminotransferase deactivates GABA…. Inhibition
of this enzyme will accumulate GABA ….Anticonvulsant
action
 Xanthine will be oxidized into uric acid…. Inhibition of
this enzyme will help in Gout patients
Enzyme inhibition
 Enzyme inhibitors in contrast to receptor antagonists,
are closely similar inn structure to enzyme natural
substrate……. It should be strongly bind to enzyme
active site….inhibiting the binding of substrate.
 Ideal Enzyme inhibitor should:
 be specific for one target enzyme
 target essential enzymes in essential metabolic pathway
 Selectively inhibit essential enzymes in non human cells
that are unique, does not exist in human cells or duite
different in structure
Drug synergism
 When two drugs are given in combination, the
therapeutic effect of them is greater than the sum of
their effects if they are given individually.
 Mechanisms of enzyme synergism:
 inhibition of drug destroying enzymes:
Example: calvulanic acid with amoxicillin
 Sequential blocking:


Inhibiting two or more consecutive steps or enzymes in the
same metabolic pathway
Example: Trimethorprim with sulfamethoxazole