Enzymes as drug targets

Question 1

Enzymes

Answer 1

protein molecules, catalyse a specific reaction, unchanged by the reactions they catalyse

Question 2

how does enzyme work as catalyst?

Answer 2

providing an alternative pathway for the reaction in which the rate-determining step has a lower Gibbs activation energy than that of the non-catalysed reaction

Question 3

steps in enzyme kinetics;

Answer 3

1) reversible
2) irreversible

Question 4

What is The Michaelis Menten Equations?

Answer 4

( 𝒅[𝑬𝑺])/𝒅𝒕=k1 [E] [S] –(k2 - k-1 )[ES]=0

[E]0 = [ES] + [E]

𝑽 (𝒓𝒂𝒕𝒆 𝒐𝒇 𝒓𝒆𝒂𝒄𝒕𝒊𝒐𝒏)= ( 𝑽𝒎𝒂𝒙 [𝑺])/(𝑲𝑴+[𝑺])

[S] is effectively constant

Question 5

Define Vmax or (rate)max

Answer 5

maximum velocity the reaction can achieve. It is equal to K2[E]0

Question 6

What is Km?

Answer 6

the Michaelis constant. It is (k2 +k-1)/k1

Question 7

The velocity (rate) of an enzyme catalysed reaction increases in a __________ fashion

Answer 7

non-linear

Question 8

When [S] is large, [S]

Answer 8

> > Km

Question 9

Maximal Velocity Vmax

Answer 9

𝑽 (𝒓𝒂𝒕𝒆 𝒐𝒇 𝒓𝒆𝒂𝒄𝒕𝒊𝒐𝒏)= ( 𝑽𝒎𝒂𝒙 [𝑺])/([𝑺]) = Vmax = K2 [E]0

[s] cancel each other

Question 10

What is the turnover number?

Answer 10

number of substrate molecules converted into product by an enzyme molecule in a unit time when the enzyme is fully saturated with substrate

Question 11

what is the connection between the Vmax and k2?

Answer 11

Vmax and is equivalent to the rate constant k2.

Question 12

turnover number equation?

Answer 12

K2 = Vmax/[E]0 (s-1)

Question 13

turnover numbers of most enzymes with their physiological substrates fall in the range from:

Answer 13

1 to 10^4 s-1

Question 14

KM gives an indication of how _______ the enzyme binds its substrate

Answer 14

tightly

Question 15

Weak substrate, large KM

Answer 15

high [S] is needed to achieve Vmax/2 (and even more to reach Vmax!)

Question 16

Good substrate, low KM:

Answer 16

Only a low [S] needed to reach Vmax.

Question 17

Enzymes as drug targets - altered metabolic pathway

Answer 17

excess or deficiency of a specific metabolite.

Question 18

Irreversible enzyme inhibitors: what type of bonding?

Answer 18

bind covalently to an enzyme,
or form a highly stable non-covalent association (tight-binding inhibitors)

Question 19

name an Irreversible enzyme inhibitor?

Answer 19

Penicillins: irreversible enzyme inhibitors specific for a bacterial enzyme (peptidoglycan transpeptidase), needed to build the bacterial wall

Question 20

name an Irreversible enzyme inhibitor?

Answer 20

Penicillins: irreversible enzyme inhibitors specific for a bacterial enzyme (peptidoglycan transpeptidase), needed to build the bacterial wall

Question 21

Suicide inactivators or mechanism-based inactivators:

Answer 21

irreversible inhibitors (covalent): one drug molecule completely inactivates one enzyme molecule, and it is lost in the process

Question 22

How to make inhibitors MORE selective for target? LESS side effects

Answer 22

1) Initially binds reversibly (Intermolecular bonding interactions), then if molecule is held long enough irreversible interactions take place

2) use mildly reactive electrophilic groups

Question 23

Irreversible enzyme inhibitors - strength

Answer 23

EFFECTED by; drug concentration and time after administration we measure the enzyme activity (→how quickly can the drug inhibit the enzyme)

Question 24

Reaction of kinetics = step by step?
ADD increasing inhibitor concentrations.

Answer 24

1. as [inhibitor] increases, the maximum amount of product formed decreases;
2. as [inhibitor] increases, the inactivation rate increases
   (curve of P formation drops off faster)
3. time passes, more enzyme molecules have been inactivated (greater deviation from uninhibited reaction)

> > > > >

good irreversible inhibitor must be specific and inactivate the enzyme rapidly

Question 25

What type of bond is used for a reversible enzyme inhibitor?

Answer 25

non-covalent {or reversible covalent}: diffuse in and out of enzymes. Enzyme may bind its substrate (ES complex), or the inhibitor (EI complex). Once one is bound, the other may also bind (ESI complex). Only ES complex is catalytically active

Question 26

KI (inhibitor dissociation constant): lower KI > _______ binding >
more effective inhibitor

Answer 26

tighter

Question 27

Turnover Number = K2 = Vmax/[E]0 (s-1) while Km =

Answer 27

[S] at ½ Vmax

Question 28

list the 3 main types of reversible inhibitors?

Answer 28

1. competitive
2. uncompetitive
3. mixed

Question 29

Competitive inhibitors

Answer 29

bind the same site of the substrate (active site) and prevent the substrate from binding

Question 30

Why will competitive inhibitor NOT effect Vmax?

Answer 30

enough substrate is present, it will out-compete the inhibitor and saturate the enzyme

Question 31

Why will competitive inhibitor ^ Km?

Answer 31

higher [S] to saturate the enzyme when the inhibitor is present

Question 32

competitive inhibitors are similar to substrates;
give example

Answer 32

xylose: prevents binding of glucose to hexokinase (phosphorylation of glucose hydroxymethyl group)

Xylose can make the same interactions as glucose with the active site residues, but it does not have a reactive hydroxymethyl group > it cannot react

Question 33

GRAPH: As [I] increases, the curvature becomes

Answer 33

shallower - although all curves would reach Vmax if [S] is enough

Smaller KI > greater drop in V0

Question 34

Uncompetitive inhibitors - decrease Vmax and decrease Km:

Answer 34

increasing [S] makes the inhibitor more effective (Vmax decreases) because it binds to ES

Question 35

Uncompetitive inhibitors - Km is also decreased

Answer 35

apparent affinity of E for S is increased: formation of ESI complex pulls the equilibrium for ES formation to the right

Question 36

uncompetitive inhibitors:

Answer 36

bind a different site to the substrate: anywhere on the protein, but usually not the active site

Question 37

What do we call the change that happens to the active site when an uncompetitive inhibitor binds?

Answer 37

conformational = prevents enzyme from functioning

Question 38

As uncompetitive inhibitors decrease Vmax

Answer 38

Km - decreases

they can easily be distinguished from competitive ones looking at the effect on enzyme kinetics:

Question 39

depending on KI relative values - Vmax will always decrease, Km?

Answer 39

inc or decrease

kinetic behaviour present competitive and uncompetitive inhibition

Question 40

mixed inhibitors

Answer 40

1. decrease Vmax
2. increase/ decrease Km

Question 41

Special case of mixed inhibition: when

Answer 41

KI = KI

Question 42

What effect does non-competitive inhibitors have on km and Vmax

Answer 42

1. NOT effect Km
2. decrease Vmax