Drug-enzyme interaction

IntroductionEnzymes 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 Substrate

E S

E-S complex Product

Enzyme Active siteSubstrate binds to small area in enzyme

structure known as active site:Other names: Binding site, Binding domain,

Active pocket

Enzyme Active siteTwo types of amino acids available inside

enzyme acite site:Catalytic amino acids: directly or indirectly

participate in enzyme-substrate interactionsNon-catalytic amino acids:

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 CatalysisIs characterized by:

SpecificityRate acceleration

Reaction specificity: can be classified as:Reaction specificitySubstrate specificity

Rate acceleration is due to the presence of Co-enzymes in most of the cases

Co-EnzymesAre any organic molecules or metal ions that

are essential for catalytic action of enzyme.Examples:

ATPCoenzyme AGlutathioneAscorbic acidLipoic acidZn, Co, Fe, Mg cations

ATP exists in the active site of ATP-dependent phosphofructokinase

Substrate specificitySubstrate 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 othersDifferent amino acids in active site play a

major role in specificity.

Binding specificitySub-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 groupHO

HO

HN

OH

COMT

SAM

O

HO

HN

OH

Binding specificityDeterminant 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 specificitySub-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: 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

Val

OOC NH3

NH3COO

H

Val

OOC NH3

NH3COO

H

Favored interaction

Steric clash between benzene ring and valine residue

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

Enzyme (E) + Substrate (S)

R isomer S isomerR isomer

E-S complexR S or RR

Diastereomers

Product

The most stable diastereomers will beenergetically favored to be formed

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.

NH2

HH

R1R2

Binding amino acid for R2Binding amino acid for R1

Rate accelerationEnzyme accelerate reactions by:

Stabilizing the reaction transition state…. This will lower the activation energy.

By destabilizing drug moleculeBring 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 turnoverIs 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

Clas

sific

ation

of a

min

o ac

ids

Enzyme inhibitionEnzyme inhibitor: will slow down or block

enzyme catalysisMainly irreversible ……. Enzyme inactivationThe 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 inhibitionEnzyme inhibitor: will slow down or block

enzyme catalysisMainly irreversible ……. Enzyme inactivationThe 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 inhibitionEnzyme 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 enzymetarget 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 synergismWhen 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 amoxicillinSequential blocking:

Inhibiting two or more consecutive steps or enzymes in the same metabolic pathway

Example: Trimethorprim with sulfamethoxazole

Pteridine + PABA

Dihydropteroate synthetaseBlocked by sulfonamides

Dihydropteroic acid

Glutamate

Dihydrofolate

Dihydrofolate reductase

Tetrahydrofolate

Inhibited by trimethoprim