Understanding Enzymes and Transition State Analogs: Mechanisms and Applications

so when we introduced enzymes we said that what enzymes do is they catalyze they speed up the rates of reactions and

the way that they speed up the rates of reactions is by decreasing the energy of the transition state so in that

particular reaction that the enzyme catalyzes once that substrate is inside the active side when the reaction takes

place inside the active side what the active side does is it stabilizes the transition State and decreases the

energy of that transition state and that's exactly what lowers the activation energy that gives energy of

Activation so enzymes catalyze reactions by stabilizing the transition state within that particular reaction and

remember transition states are these structures that are so high in energy that they exist only for a very short

period of time so in that energy diagram the transition state is the topmost portion of that energy diagram now

previously we discussed different types of enzyme Inhibitors and we said that a very good enzyme inhibitor is an

inhibitor that resembles the structure of that substrate so if the inhibitor of some particular enzyme resembles the

structure of the substrate that binds into the active side of the enzyme then what that inhibitor can do is because it

has a a similar shapee to the substrate it can easily accommodate itself into that structure of the active SES so we

previously saw that a good way to inhibit the activity and the functionality of enzymes is to create an

inhibitor that resembles that natural substrate of that particular enzyme now because of the argument that we just

mentioned earlier so since enzymes active sides essentially stabilize the structure structure of the transition

state then that must imply that a much more effective and a much better inhibitor of an enzyme would be an

inhibitor that resembles not the structure of the substrate but rather the structure of the transition state

and these types of Inhibitors are known as transition state analoges or transition state Inhibitors so we see

that these transition state analoges are molecules that resemble the structure of the transition state and because enzymes

ultimately stabilize the energy in the structure of the transition state these are very very potent very effective

Inhibitors so let's take a look at two examples so let's begin by examining an enzyme found in bacterial cells known as

Proline rimas and Proline rimas basically catalyzes the transformation the isomerization reaction of el Proline

into D Proline now the difference between L Proline and D Proline lies in the stereochemistry of this Carbon on

this particular molecule the H atom points into the board but in this particular case the H atom is coming out

of the board and so that's the difference between L Proline and D Proline and Proline rmes basically

catalyzes the transformation of these two molecules back and forth now if we examine the transition state when going

from L Proline to D Proline this is what we see this is the structure of that high energy transition state and notice

that in this transition state this carbon atom has planer so is trigonal planer and what that means is these

three bonds so this coent bond this calent Bond and this Cove valent Bond all lie along the same plane and that's

what we mean by trigonal planarity so there is trigonal planarity within this molecule and what that means is so if

the H atom is added on the top side we basically form this D Proline but if the H atom is added from the bottom side

we're going to form that L Proline so from the discussion above if we can somehow build a molecule that is a

transition state analog that resembles the structure of this particular molecule then that means that transition

state analog will be a very potent inhibitor of this enzyme the proline rimas because that transition analog

that transition state analog will be able to accommodate quite easily into the active side of that enzyme so once

again the transition state of this reaction that's uh the isomerization of L Proline to D Proline contains an alpha

carb that has planer or trigonal planer that is trigonal planer and it turns out that

if we use a molecule known as perole to carboxilic acid which basically also contains trigonal planarity on that

carbon as seen in the following diagram then this will be a very very potent inhibitor and this is in fact a

transition state analog for this enzyme so let's take a look at parole 2 oxyc acid and compare the structure to the

transition state of this particular reaction so notice this carbon has trigonal planarity and so does this

carbon so because we have this double bond that means these three bonds will all lie along the same exact plane and

so these two molecules in fact resemble one another much more than this molecule resembles that substrate and because of

that because this inhibitor res resembles the transition state much more than it does that actual substrate

molecule this will be in much more potent much better inhibitor in fact this molecule here the transition state

analog perole 2 carboxilic Acid binds 160 times more likely to the enzyme's active side to the proline racm active

side than the proline molecule itself and so if given a chance this will be much more likely to bind

into the active side than this substrate molecule or this substrate molecule another example is shown on this side of

the board so the enzyme methylthioadenosine nucleus nucleus adase is basically the

enzyme that catalyzes the hydrolysis of the bond between this Carbon on the sugar molecule and this nitrogen on the

base and this reaction is known as deenal so this enzyme catalyzes the deaden

alation reaction basically the breaking of this particular bond in this molecule and so by the same argument if we are

able to build a molecule a transition state analog that resembles the structure of the transition state in

this reaction in this deadenylation reaction then we can build a very very potent inhibitor to this enzyme in fact

we can build this small molecule that will act as a transition state analog and notice there is a great deal of

similarity between this molecule and this transition state now the final question that I want

to discuss is what exactly is the usefulness of this transition state analog so one usefulness is the ability

to build a molecule that is a very good inhibitor to some particular type of enzyme so for instance if a bacterial

cell if a bacteria infects our body then one way to inhibit the activity of that bacterial cell is to inhibit in some way

some type of enzyme by using transition state analoges now another important

application of transition state analoges is the following we can actually create antibodies that have specific cat

catalytic capabilities by using these transition state an analog so we can now build antibodies with specific catalytic

capabilities by using transition state analoges as antigens and to demonstrate how this actually works let's discuss

the biosynthesis process the biosynthesis of the heem groups so remember in proteins such as hemoglobin

and myoglobin we have these important prosthetic groups known as heem groups and at the center of the heem group is

the protop porphin ring so the protop porphin ring basically is that organic part of that hm group that actually

carries that holds that iron atom now in the process of the synthesis of this protop porphin ring of the H group the

final step is to basically use a special enzyme known as ferocitas to basically catalyze the

insertion of that Fe atom the metal atom into the center of the protop ring now normally the protop porphin ring has a

planer shape so the shape of it is relatively planer but to actually fit that Fe atom the metal atom into the

center of that protop porphine what this enzyme does what the ferocitas does is it basically bends the shape of that

protop porphin ring and then that exposes the uh the electrons the lone pair of electrons that can now find that

Fe atom and so what the Ferro ketas does is it basically catalyzes the bending of that planer shape of the protopine

molecule and that allows the fitting that allows the insertion of that Fe atom into that he group into that protop

porphin now how can we use this to basically build an antibody with a specific type of catalytic ability well

normally the protop porphine has a planer shape and we see that what this en what this enzyme does is it basically

bends the sh bends the shape and so the transition state of the protop porin Ring has to be bent in shape so the

transition state of the protop porphin basically has a Bend shape so that means if we can somehow build a transition

state analog that has the protop porphin with a Bend shape that means that type of molecule will be much more likely to

bind into the active side of that particular enzyme the Ferro kelate so in fact what we can do is we can methylate

one of the nitrogen atoms in that ring and by methylating this nitrogen that creates steric hindrance and that forces

the bending of that protop porphin rink and now that we have formed this transition state analog whose structure

resembles the transition state structure in that particular uh catalytic process we can now expose we can use this

molecule this transition state analog as an antigen essentially expose it to a plasma cell the plasma cell will in turn

basically begin building antibodies that contain an active side that has a complimentary structure to this

particular antigen and so once we build that anti anbody the antibody will be easily able to fit those protor

molecules into the antibody active side and that antibody will in turn have the catalytic ability to basically transform

or insert that Fe atom into the center ring of that particular protop porphin so we see that transition state analoges

are not only useful in actually inhibiting and blocking the ability of enzymes to catalyze reactions but we can

also use these transition state analoges to actually build antibodies that have catalytic capabilities and these

antibodies are commonly known as abzymes where AB stands for antibody and the zy part stands for the enzyme so abzymes

are these antibodies that contain catalytic capabilities that can basically catalyze different types of

reactions and the way that we build them is by using these transition state analoges as antigen molecules