Explanation of the PCP site

[Lightning-Nl]

After doing immense reading on the N-Methyl-D-Aspartate Receptor, I'm still unable to grasp the concept of the PCP site. From what I can gather about it, it's located inside the ion channel and it's a non-competitive binding site. Due to the fact that it's located inside the ion channel - that leads me to assume that it's actually an allosteric site? Rather than an active site where endogenous ligands bind to?

Also there was a ton of weird information (that I kind of skipped through since I'm pretty loaded on Temazepam at the moment) However, I'd still appreciate a solid explanation of this unique binding site that I'm not quite getting my head around.

Thanks for the info guys!

SwampFox

 

[nAON]

Basically yeah. It's a non-competitive channel blocker. Ketamine binds similarly.

 

[Lightning-Nl]

So could antagonists at this binding site technically be termed "Negative Allosteric Modulators"? Or would that be reserved for chemicals that still allow the ion channel to function to some extent?

 

[nAON]

I think to be classed as an allosteric modulator, it has to affect endogenous ligand binding in some way, ie. by potentiating/inhibiting glutamate effect, or by altering desensitization properties. Dunno the exact semantics but I usually imagine channel blockers as being in their own group.

 

[sekio]

In biochemistry, allosteric regulation is the regulation of an enzyme or other protein by binding an effector molecule at the protein's allosteric site (that is, a site other than the protein's active site).

So yeah, I guess they are, technically speaking, negative allosteric modulators. Although this effect comes from a physicochemical blockade rather than a distortion of the protien shape, e.g. rather than forcing the channel to close/open on its own or making it more susceptible to (like benzos), the ketamine/PCP/DXO or whatever actually physically impedes the ion traffic through the already-opened pore with its molecular bulk.

 

[ebola?]

Do we have examples of negative allosteric modulators at NMDA that do not block the ion channel? I've found digging through secondary sources kind of confusing before (some, for example, mistakenly deeming ketamine/DXM/PCP to have different mechanisms).

ebola

 

[Lightning-Nl]

Thanks for the explanation. Didn't know that 'non-competative' was the same thing as 'channel blocker' (well I did know that, but I didn't know that their mechanisms of action were identical) That makes me curious...

For substances that are specifically classified as "channel blockers" - do they do so at every channel then? What I mean by this is - let's say we have a Calcium Channel Blocker, and we have a non-competative NMDA antagonist. The NMDA antagonist will stop the inflow of Clacium at the NMDA ion channel.

Now we have the Calcium Channel Blocker - will these types of drugs inhibit calcium influx directly at the receptors? Or does it block the calcium 'transporters' (for lack of a better word) like I initay thought they did? If my first question is correct - Could this drug be considered a drug that antagonizes all receptors that allow inflow of Calcium into a cell?

 

[sekio]

Now we have the Calcium Channel Blocker - will these types of drugs inhibit calcium influx directly at the receptors? Or does it block the calcium 'transporters' (for lack of a better word) like I initay thought they did? If my first question is correct - Could this drug be considered a drug that antagonizes all receptors that allow inflow of Calcium into a cell?

Calcium channel blockers bind to and inhibit the flow of ions through a specific protien called the calcium channel... of which there are many subtypes. It's a general term.

NMDAr is not considered a calcium channel because it permits more than Ca2+ to flow though it, NMDA antagonists do not substitute for Ca channel blockers, and it lacks genetic similarity to the other Ca2+ channels.

 

[Lightning-Nl]

Calcium channel blockers bind to and inhibit the flow of ions through a specific protien called the calcium channel... of which there are many subtypes. It's a general term.

NMDAr is not considered a calcium channel because it permits more than Ca2+ to flow though it, NMDA antagonists do not substitute for Ca channel blockers, and it lacks genetic similarity to the other Ca2+ channels.

Don't worry, I know that NMDAr isn't part of the calcium channel and that it lets in more than just calcium. Unfortunaetly, I worded my question incorrect (which, I'm noticing, seems to keep happen after I've plugged a dose of amphetamine...) But anyways, you answered my question - Ca channel blockers are, in fact, inhibiting channels that are designed specifically, to only carry Ca2+ through the channel.

 

[ebola?]

Thanks for the explanation. Didn't know that 'non-competative' was the same thing as 'channel blocker'

That's not right, in that there are various types of non-competitive and competitive agonists and antagonists (many of which function as allosteric modulators of various sorts). A competitive agonist simply binds at a receptor in a way that precludes binding of the endogenous ligand.

ebola

 

[Lightning-Nl]

That's not right, in that there are various types of non-competitive and competitive agonists and antagonists (many of which function as allosteric modulators of various sorts). A competitive agonist simply binds at a receptor in a way that precludes binding of the endogenous ligand.

ebola

I don't really know how you got that assumption out of my post. Anyways, I'm well aware of what competitive and non-competitive refer to. What my post was saying is that I was unaware that non-competitive antagonists, essentially have the same function as a channel blocker.

 

[Hammilton]

What else would an antagonist do to an ionotropic receptor?

 

[nAON]

Do we have examples of negative allosteric modulators at NMDA that do not block the ion channel? I've found digging through secondary sources kind of confusing before (some, for example, mistakenly deeming ketamine/DXM/PCP to have different mechanisms).

ebola

Eliprodil acts as NAM for NMDA by binding at dimer interface site. Can't remember any others off top of head.

 

[Lightning-Nl]

What else would an antagonist do to an ionotropic receptor?

Good point. I guess I just didn't think it through tbh. A neutral antagonist, I know doesn't interfere with ion channel function like true antagonists do. If I remember correctly - they still allow the ion channel to function but antagonize a receptor through competitive binding. They literally just don't allow the agonizing ligand to bind because their occupying the active site - and yet, they have no effect on ion channel function.

Sounds sort of weird now that I've typed that out. But that's what I remember reading on how neutral antagonists function. Better to read the information on it again though...

 

[specialspack]

Do we have examples of negative allosteric modulators at NMDA that do not block the ion channel? I've found digging through secondary sources kind of confusing before (some, for example, mistakenly deeming ketamine/DXM/PCP to have different mechanisms).

ebola

I assume you're talking about the wikipedia page here:
http://en.wikipedia.org/wiki/NMDA_receptor_antagonist

Which differentiates non-competitive antagonists (negative allosteric modulators) and uncompetitive antagonists (channel blockers).

And then goes and sticks ketamine in the non-competitive group, and PCP, MXE, DXM et al in the uncompetitive group, which makes not a bit of sense.

I've not really found much good backup for this distinction, indeed many papers seem to use noncompetitive and uncompetitive synonymously.

As for non channel blocker antagonists - drugs that bind to the glycine site for starters?

The other thing that's always confused me - is the Mg2+ site the same as the PCP site, or different? They're both located inside the channel...

 

[nAON]

I assume you're talking about the wikipedia page here:
http://en.wikipedia.org/wiki/NMDA_receptor_antagonist

Which differentiates non-competitive antagonists (negative allosteric modulators) and uncompetitive antagonists (channel blockers).

And then goes and sticks ketamine in the non-competitive group, and PCP, MXE, DXM et al in the uncompetitive group, which makes not a bit of sense.

I've not really found much good backup for this distinction, indeed many papers seem to use noncompetitive and uncompetitive synonymously.

As for non channel blocker antagonists - drugs that bind to the glycine site for starters?

The other thing that's always confused me - is the Mg2+ site the same as the PCP site, or different? They're both located inside the channel...

Pretty sure the specific point in the channel is different for Mg2+ and PCP/ket etc.

 

[crOOk]

Didn't know that 'non-competative' was the same thing as 'channel blocker'

It's not. There doesn't even have to be an ion channel associated with the proteine the non-competitive inhibitor inhibits. For an enzyme inhibitor to be considered "non-competitive" it simply has to have the same affinity to the proteine, whether the proteine has it's ligand bound to it or not. Therefore, a non-competitive inhibitor always binds allosterically (at another binding site than the active site). But it doesn't need to block an ion channel. Enzymes can have all kinds of functions other than allowing ion flux through membranes.

Whichever way you look at it, the pcp binding site remains a very awesome binding site if you intend to get fucked up.

EDIT: About uncompetitive inhibition, there is a clear distinction. A substance inhibits an enzyme uncompetitively, when the former only binds to the latter AFTER the enzyme's substrate is bound to it. The non-competitive inhibitor doesn't care, it always binds to the enzyme with the same affinity, the uncompetitive ONLY when the active site has it's ligand in place and the "competitive inhibitor" ONLY binds to the enzyme when there is NO substrate at the active site (or the substrate dissociates from the enzyme if it had it's substrate bound to the active site). That's why the competitive inhibitor is called competitive, it competes with the substrate for the active binding site, while the uncompetitive and non-competitive inhibitors bind allosterically (at another site than the active one).

EDIT2: Since the PCP binding site is within the channel, PCP can only bind when the channel is open/active. This is only the case when glutamate has bound to the receptor. Therefore PCP should be an uncompetitive inhibitor and not a non-competitive one. Correct me if I am wrong.

EDIT3:

And then goes and sticks ketamine in the non-competitive group, and PCP, MXE, DXM et al in the uncompetitive group, which makes not a bit of sense.

It does make sense because there is another allosteric binding site for ketamine. It does not (only?) bind to the PCP binding site.

 

[specialspack]

EDIT3: It does make sense because there is another allosteric binding site for ketamine. It does not (only?) bind to the PCP binding site.

What are the references for this?

 

[crOOk]

What are the references for this?

Anesthesiology. 1997 Apr;86(4):903-17.
Multiple mechanisms of ketamine blockade of N-methyl-D-aspartate receptors.

I'm sure you'll find more up-to-date information on this.

The thing is, I could still neither really classify ketamine as purely non-competitive, nor as uncompetitive. If it can only bind to the PCP site when the channel is open, this would mean it's not non-competitive in that it has a different affinity to the proteine when there's glutamate present than when there is none, shouldn't it? On the other hand it's not really uncompetitive since it can also bind to the other binding site outside of the ion channel when there the channel is closed. After all, it doesn't really matter that much because these categories are only meant to give you an idea of the kinetics. For stuff like ketamine you would just have to look at them separately. Just like mushrooms are neither animal, nor plant, the categories are limited in their descriptive power.

 

[specialspack]

Anesthesiology. 1997 Apr;86(4):903-17.
Multiple mechanisms of ketamine blockade of N-methyl-D-aspartate receptors.

I'm sure you'll find more up-to-date information on this.

Hmmm... I can't find any other papers discussing this secondary allosteric mechanism for ketamine. I'm not convinced on the strength of one paper from 1997.