March 29, 2024, 09:52:08 AM
Forum Rules: Read This Before Posting


Topic: Transition State Analogs  (Read 7504 times)

0 Members and 1 Guest are viewing this topic.

Offline qw098

  • Full Member
  • ****
  • Posts: 141
  • Mole Snacks: +5/-0
Transition State Analogs
« on: April 19, 2012, 11:02:26 AM »
Hi,

Quick juvenile question about transition state analogs... mainly just my brain thinking...

So, if a transition state analog does NOT bind covalently to the enzyme, so how exactly does it act as an inhibitor. My theory is that it simply enters the active site of the enzyme and hydrogen bonds with the active site residues of the enzyme, or can also can bind in the specificity pocket of the enzyme (ie: hydrophobic specificity pocket).

Is my "theory" the accepted theory/explanation for how transition state analogs actually function as inhibitors?

Thanks!

PS My same "theory" would still hold for substrate analogs I believe as well, eh?

Offline Babcock_Hall

  • Chemist
  • Sr. Member
  • *
  • Posts: 5592
  • Mole Snacks: +319/-22
Re: Transition State Analogs
« Reply #1 on: April 19, 2012, 12:24:59 PM »
I think your model is a little too specific with respect to the intermolecular forces.

Offline qw098

  • Full Member
  • ****
  • Posts: 141
  • Mole Snacks: +5/-0
Re: Transition State Analogs
« Reply #2 on: April 19, 2012, 12:32:56 PM »
I think your model is a little too specific with respect to the intermolecular forces.

What would you suggest?

I simply used hydrogen bonds as an example of the possible intermolecular forces that could be present.

But as a whole, is my model/theory the "accepted" theory of how these transition/substrate analogs bind to the enzyme / act as inhibitors?

Thanks!


Offline dipesh747

  • Regular Member
  • ***
  • Posts: 89
  • Mole Snacks: +7/-7

Offline qw098

  • Full Member
  • ****
  • Posts: 141
  • Mole Snacks: +5/-0
Re: Transition State Analogs
« Reply #4 on: April 19, 2012, 02:17:33 PM »
Yes, I have seen that page before.

It however doesn't explain how exactly the transition-state analogs are binding. I know they don't bind covalenty which means there won't be any nucleophilic attacks or any "arrow pushing" mechanism lik e the usual substrate would end up doing with the enzyme.

So how exactly do these transition-state analog bind to the enzyme non-covalently (?), perhaps via other interactions such as hydrophobic, hydrogen bonding... etc? The transition-state analog just "sits" there in the active site (?)

Offline Babcock_Hall

  • Chemist
  • Sr. Member
  • *
  • Posts: 5592
  • Mole Snacks: +319/-22
Re: Transition State Analogs
« Reply #5 on: April 19, 2012, 04:11:19 PM »
I would say that some transition state analogs do not bind covalently (perhaps the majority), but other do.  There are several classes of t.s. analogs of the serine proteases (peptidyl aldehydes, peptidyl trifluoromethylketones, and peptidyl boronates) that form a covalent bond to the enzyme when the serine nucleophile adds into the electrophilic atom.  The bond is easily broken, however, and the normal substrate also forms a covalent bond with the enzyme.

Offline qw098

  • Full Member
  • ****
  • Posts: 141
  • Mole Snacks: +5/-0
Re: Transition State Analogs
« Reply #6 on: April 19, 2012, 04:23:31 PM »
I would say that some transition state analogs do not bind covalently (perhaps the majority), but other do.  There are several classes of t.s. analogs of the serine proteases (peptidyl aldehydes, peptidyl trifluoromethylketones, and peptidyl boronates) that form a covalent bond to the enzyme when the serine nucleophile adds into the electrophilic atom.  The bond is easily broken, however, and the normal substrate also forms a covalent bond with the enzyme.

Yes, ok great. Things like diisopropylfluorophosphate (DIFP) are transition-state analogs, but interestingly enough, are placed in the irreversible inhibitor category. DIFP reacts covalently with Serine 195.

Typically transition-state analogs are reversible inhibitors (do not bind covalently).

Offline dipesh747

  • Regular Member
  • ***
  • Posts: 89
  • Mole Snacks: +7/-7
Re: Transition State Analogs
« Reply #7 on: April 19, 2012, 08:40:56 PM »
Ok why can these analogs not bin covalently? Looking on that website it appears there would at minimum be covaleant attraction which would inevitbley result in a covalent bond. Inter molecular forces won't play much of a part (relatively) when you have an anion on a molecule. Do you have an exact example you want to talk about. You can't just generally talk about all TS analogs, they will have different chemistry associated with them.

I would have thought that they bind more strongly because their geometry is similar to that of a substrare TS, but much more stable which would result in high energy needed to break that bond. (If you think about potential energy surfaces there would have to be an energetic reason why the substrate would provide the energy to form that TS)

I don't really know anything specifically about this I have just read that one paragraph on the web link but thats what it seems like to me.

Offline orgopete

  • Chemist
  • Sr. Member
  • *
  • Posts: 2636
  • Mole Snacks: +213/-71
    • Curved Arrow Press
Re: Transition State Analogs
« Reply #8 on: April 20, 2012, 12:35:12 AM »
The reference seems more than adequate to answer the question.

"16.5  • Transition- State Analogs Bind Very Tightly to the Active Site

Although not apparent at first, there are other important implications of Equation 16.3. It is important to consider the magnitudes of KS and KT. The ratio ke/ ku may even exceed 1016, as noted previously. Given a typical ratio of 1012 and a typical KS of 10-3 M, the value of KT should be 10-15 M! This is the dissociation constant for the transition-state complex from the enzyme, and this very low value corresponds to very tight binding of the transition state by the enzyme."

If the transition state binds at 10-15 M, do you really need a covalent bond?
Author of a multi-tiered example based workbook for learning organic chemistry mechanisms.

Offline qw098

  • Full Member
  • ****
  • Posts: 141
  • Mole Snacks: +5/-0
Re: Transition State Analogs
« Reply #9 on: April 20, 2012, 05:40:40 AM »
If the transition state binds at 10-15 M, do you really need a covalent bond?

Yes, precisely orgopete. I saw that on the page. I guess what I am really after... is... what type of interactions are occurring when the transition state "binds". Are they indeed like what I said... intermolecular forces such as hydrophobic interactions, hydrogen bonding etc...

Offline Babcock_Hall

  • Chemist
  • Sr. Member
  • *
  • Posts: 5592
  • Mole Snacks: +319/-22
Re: Transition State Analogs
« Reply #10 on: April 20, 2012, 09:33:14 AM »
I think that the full panoply of intermolecular forces are possible and some subset of them will be seen in any particular case.  Consider that avidin binds to biotin with a dissociation constant that is estimated at 10^-15, and this is a noncovalent interaction.

Offline orgopete

  • Chemist
  • Sr. Member
  • *
  • Posts: 2636
  • Mole Snacks: +213/-71
    • Curved Arrow Press
Re: Transition State Analogs
« Reply #11 on: April 20, 2012, 11:20:24 AM »
I am currently writing to explain the energy differences Pauling was trying to explain with his theory of electronegativity. There is a paradox one must deal with. According to Pauling theory, bonds contain ionic and covalent character. If polar bonds are stronger than covalent bonds, NaCl has a high heat of formation and a high melting point, we can think they are strong. Yet, ionic bonds are easily broken by dissolving in water. We may think hydrogen bonds are weak, yet you can drive your car on ice. Ultimately, bond strengths are going to come to charge and distance considerations. When that happens, bond types disappear. A covalent bond to t-butyl iodide may be weaker than an ionic bond to calcium fluoride. Protons are positive and electrons negative. If a proton can come in close proximity to an electron pair, its attractive force can be greater. Presumably this is at least in part what is happening in ice. It is also forming a matrix of bonds. A matrix can be much stronger than an individual bond. A bridge of toothpicks can be much stronger than an individual toothpick.

I can imagine an enzyme-substrate complex being more like a matrix than measuring an individual bond. If so, the combined effect of many seemingly weaker bonds may result in great affinity. Also, even seemingly weak hydrogen bonds (or any other interaction) becomes stronger with the inverse square of the distance.

The affinity cited in the referenced link are more like irreversible inhibitors. Even the substrate should inhibit the enzyme. However, if the reaction proceeds, the transition state can become the product. The binding of the product must be much lower in order for the enzyme to turn over the substrate. That must happen.
Author of a multi-tiered example based workbook for learning organic chemistry mechanisms.

Offline qw098

  • Full Member
  • ****
  • Posts: 141
  • Mole Snacks: +5/-0
Re: Transition State Analogs
« Reply #12 on: April 20, 2012, 02:46:44 PM »
PRECISELY what I was looking for orgopete!

Great stuff! Thanks as always!

Offline Babcock_Hall

  • Chemist
  • Sr. Member
  • *
  • Posts: 5592
  • Mole Snacks: +319/-22
Re: Transition State Analogs
« Reply #13 on: April 24, 2012, 07:56:05 PM »
I have two general comments on transition state analogs.  One is that I have heard it said that distinguishing between a bisubstrate analog and a true transition state analog can be difficult.  Both can bind tightly, so that is not a good way to differentiate the two.

Two is that it is sometimes possible to study a series of structurally related substrates (to find the rates as kcat/Km) and also to study an analogous series of structurally related inhibitors (to find the Ki values).  If the rates and the inhibitory constants correlate well, then the series of compounds are transition state analogs.  For an example using the protease thermolysin, see http://www.ncbi.nlm.nih.gov/pubmed/6626519.  For peptidases, one varies the identity of one of the amino acid residues in a short, synthetic substrate and one also varies the same amino acid residue in the inhibitor.

Sponsored Links