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Can someone explain the logic behind this binding profile??

JohnBoy2000

JohnBoy2000

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May 11, 2016
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Amitriptyline is suppose to act more on sertonin and less on noradrenaline.
Nortriptyline, the other way around.
Why are the binding values for SERT higher for the latter, and the NET binding values higher for the former, in that case??

Also - the binding to the mACH subrecepters is also far higher for nortriptyline - though amitriptyline is supposedly far more potent in terms of its anticholinergic side effects.

It seems like they got the binding profiles for the two drugs the wrong way around, no??
[TABLE="class: wikitable sortable jquery-tablesorter"]
[TR]
[TH="class: headerSort, bgcolor: #F2F2F2, align: center"]Receptor[/TH]
[TH="class: headerSort, bgcolor: #F2F2F2, align: center"]Ki [nM][Note 1]
(amitriptyline)[30][31][/TH]
[TH="class: headerSort, bgcolor: #F2F2F2, align: center"]Ki [nM][Note 2]
(nortriptyline)[30][31][/TH]
[/TR]
[TR]
[TD]SERT[/TD]
[TD]3.13[/TD]
[TD]16.5[/TD]
[/TR]
[TR]
[TD]NET[/TD]
[TD]22.4[/TD]
[TD]4.37[/TD]
[/TR]
[TR]
[TD]DAT[/TD]
[TD]5380[/TD]
[TD]3100[/TD]
[/TR]
[TR]
[TD]5-HT1A[/TD]
[TD]450[/TD]
[TD]294[/TD]
[/TR]
[TR]
[TD]5-HT1B[/TD]
[TD]840[/TD]
[TD]-[/TD]
[/TR]
[TR]
[TD]5-HT2A[/TD]
[TD]4.3[/TD]
[TD]5[/TD]
[/TR]
[TR]
[TD]5-HT2C[/TD]
[TD]6.15[/TD]
[TD]8.5[/TD]
[/TR]
[TR]
[TD]5-HT6[/TD]
[TD]103[/TD]
[TD]148[/TD]
[/TR]
[TR]
[TD]5-HT7[/TD]
[TD]114[/TD]
[TD]-[/TD]
[/TR]
[TR]
[TD]H1[/TD]
[TD]1.1[/TD]
[TD]15.1[/TD]
[/TR]
[TR]
[TD]H3[/TD]
[TD]1000[/TD]
[TD]-[/TD]
[/TR]
[TR]
[TD]H4[/TD]
[TD]33.6[/TD]
[TD]-[/TD]
[/TR]
[TR]
[TD]M1[/TD]
[TD]12.9[/TD]
[TD]40[/TD]
[/TR]
[TR]
[TD]M2[/TD]
[TD]11.8[/TD]
[TD]110[/TD]
[/TR]
[TR]
[TD]M3[/TD]
[TD]25.9[/TD]
[TD]50[/TD]
[/TR]
[TR]
[TD]M4[/TD]
[TD]7.2[/TD]
[TD]84[/TD]
[/TR]
[TR]
[TD]M5[/TD]
[TD]19.9[/TD]
[TD]97[/TD]
[/TR]
[TR]
[TD]α1[/TD]
[TD]24[/TD]
[TD]55[/TD]
[/TR]
[TR]
[TD]α2[/TD]
[TD]690[/TD]
[TD]2030[/TD]
[/TR]
[TR]
[TD]D1[/TD]
[TD]89[/TD]
[TD]-[/TD]
[/TR]
[TR]
[TD]D2[/TD]
[TD]1460[/TD]
[TD]2570[/TD]
[/TR]
[TR]
[TD]D3[/TD]
[TD]206[/TD]
[TD]-[/TD]
[/TR]
[TR]
[TD]D5[/TD]
[TD]170[/TD]
[TD]-[/TD]
[/TR]
[TR]
[TD]σ[/TD]
[TD]300[/TD]
[TD]2000[/TD]
[/TR]
[/TABLE]
 
Lower Ki = tighter binding = more effect at the receptor/transporter (generally). The reason for this is because the numbers are actually a measure of the concentration required to displace another ligand off the receptor when you measure Ki. EC50/IC50 are likewise the concentration needed to get a 50% effect/inhibition at a certain receptor - taking into account that some compounds will bind but produce less of an effect than others (agonist vs partial agonist vs antagonist).

One must keep that in mind when reading binding constants. It's also prudent to keep track of the units (milli versus micro versus nano) and remember that Ki is specific to the ligand used in the displacement study - comparing two different Ki values that used different ligands won't make sense.

So yeah, the reason that it seems all the effects are backwards is because you're interpeting the numbers backwards!
 
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sekio said:
Lower Ki = tighter binding = more effect at the receptor/transporter (generally). The reason for this is because the numbers are actually a measure of the concentration required to displace another ligand off the receptor when you measure Ki. EC50/IC50 are likewise the concentration needed to get a 50% effect/inhibition at a certain receptor - taking into account that some compounds will bind but produce less of an effect than others (agonist vs partial agonist vs antagonist).

One must keep that in mind when reading binding constants. It's also prudent to keep track of the units (milli versus micro versus nano) and remember that Ki is specific to the ligand used in the displacement study - comparing two different Ki values that used different ligands won't make sense.

So yeah, the reason that it seems all the effects are backwards is because you're interpeting the numbers backwards!
Click to expand...
Just to clarify, the point of converting IC50 (the ligand concentration that blocks 50% of the specific binding of the radioligand) to Ki is to make the result independent of the radioligand affinity or concentration. Hence, Ki values are not specific to the radioligand, but measure a fixed value (the ligand concentration that produces 50% occupation of a binding site at equlibrium). The issue that seiko is referring to is the fact that agonist radioligands selectively label a subpopulation of binding sites (ie, there are high and low affinity components to their binding) and therefore will yield different values compared to antagonists.
 
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The answer has already been stated but also keep in that this data is only binding profiles. While binding affinity often correlates with the effect seen they do not represent the actual effect taking place or whether it is agonism/antagonism etc. These numbers are simply a measurement of either raw binding or displacement of the normal ligand and more information is needed to give insight into the actual actions happening.
 
Alright, had to read over it a few times but, it makes sense now.

I'm still confused as to how, an antagonist, or reverse agonist, could incite the "release" of a neurochemical, however.

By example, with several drugs, they state that the antagonism of the 5-HT2c receptor, results in the release of noradrenaline and dopamine; something to the effect.

I was under the impression that all 5-HT subreceptors were associated with serotonin....??

How is that inciting a release of noradrenaline in that case?


Then, the "blockade" (whatever that means - I would assume antagonism or reverse agonism), of the alpha or alpha 2 adrenergic receptor, stimulates the release of serotonin??

Adrenergic just, from an uneducated lay persons logical perspective - you would have to imagine is associated with adrenaline/noradrenaline - yet it incites serotonin activity...??


I'm working my way through Nestor's, "basic principles of neuropharmacology".
I assume I'll stumble into this information at some point within that book?
i.e. my questions are very relevant to understanding, "the basic principles"?

That being said, if any of you care to enlighten me in the meantime - that would be swell.
 
[h=2]Mechanism of action[edit][/h]Agomelatine is a melatonin receptor agonist (MT1 (Ki=0.1nM) and MT2 (Ki=0.12nM)) and a 5-HT2C(Ki=631nM) receptor antagonist.[42] Binding studies indicate that it has no effect on monoamine uptake and no affinity for adrenergic, histaminergic, cholinergic, dopaminergic and benzodiazepine receptors, nor other serotonergic receptors

By antagonizing 5-HT2C receptors, it disinhibits/increases noradrenaline and dopaminerelease specifically in the frontal cortex. Therefore, it is sometimes classified as a norepinephrine–dopamine disinhibitor. It has no influence on the extracellular levels of serotonin.




So what that's saying is, it's effecting a serotonin specific subreceptor, yet having no effect on serotonin, but, affecting noradrenaline and dopamine.

??
 
First of all, the correct terminology is "receptor subtype" and "inverse agonist".

Second, you have to think about what serotonin and other transmitters are actually doing in the brain. Neurons release transmitters to communicate with other neurons. So the receptors for serotonin are primarily expressed by non-serotonergic cells (ie, neurons mostly talk to other cells and not to themselves). So activation of serotonin receptors can alter the activity of non-serotonergic neurons, including noradrenergic and dopaminergic neurons.

So if the normal action of the 5-HT2C receptor is to inhibit a dopaminergic neuron, and a drug blocks (antagonizes) that action, then dopaminergic activity will increase.
 
Actually looking at certain other binding profiles, or looking for, perhaps.

Wikipedia provided me with them run downs in the initial post but, for specific binding profiles relative to bupropion, agomelatin, and mocolobimide, wikipedia doesn't have entries for them.

Any links as to where I could attain that information??

I looked in Dr Stephen Stahls book of prescribing info also, but nothing relevant was there either.

Any other books that might cover in depth the binding profiles of certain drugs??


Apparently the downregulation or antagonism of the 5-HT2c receptor subtype lends itself to the disinhibition of noradrenaline and dopamine.
That specific receptor also seems to be responsible for somnolence and increased appetite (both desirable properties for me).

But again, specific data, I cannot find.

It does mention on wiki that for agomelatine, that binding affinity is... 5-HT2C(Ki=631nM) receptor antagonist.

...which is some weak shit, no??

Compared with say, mirtazapine - 39nM - as an inverse agonist.

So how is it considered effective on noradrenaline and dopamine, with such a weak property (agomelatine, that is)??

It's affinity for melatonin seems to be far stronger.
Maybe it should be marketed as a pure melatonergic, no?
 
Having a Ki of 631 nM doesn't necessarily mean that the effect is weak. Whether or not an affinity value is "weak" depends on a variety of factors.
1. What is the concentration of the drug at its site of action? If the typical concentration is 5 nM, then the affinity is low. However, if 500 nM is a typical concentration, then the situation is totally different.
2. How selective is the drug? If the drig has 10-fold lower affinity for all other sites, for example, then you can keep raising the dose until you see activity without inducing side effects.
3. For some effects, you may only need low levels of receptor occupation, so the Ki may be misleading.
 
serotonin2A said:
Having a Ki of 631 nM doesn't necessarily mean that the effect is weak. Whether or not an affinity value is "weak" depends on a variety of factors.
1. What is the concentration of the drug at its site of action? If the typical concentration is 5 nM, then the affinity is low. However, if 500 nM is a typical concentration, then the situation is totally different.
2. How selective is the drug? If the drig has 10-fold lower affinity for all other sites, for example, then you can keep raising the dose until you see activity without inducing side effects.
3. For some effects, you may only need low levels of receptor occupation, so the Ki may be misleading.
Click to expand...

Okay, say i'm looking at these binding profiles:

https://en.wikipedia.org/wiki/Pharmacology_of_antidepressants#Receptor_affinity

Now, venlafaxine's affinity for NE is, or certainly seems, quite weak, at 2753 nM.
That being said, it's affinity for other receptors is extremely week, >35000 nM.
So what you seem to be suggesting is that, due to this, the concentration of the drug itself can be pushed so much higher, so that NE binding value ultimately translates as being more potent that it appears...?

Now, next question - where is the, "drug concentration value?"

In a sense, to put perspective on the Ki values, wouldn't we need to know the overal "concentration value" - that to which you are referring above?

Or must we simply look at the other receptor Ki values and use them to put the relevant values in perspective?


By example - comparing venlafaxine with vortioxetine.

Vortioxetine is not marketed as having an effect, perhaps at all, on NE transport.
Yet its NET binding is far stronger than venlafaxine - by about 3x.

Then, it also has a much stronger binding effect on the 5HT-1A receptor subtype, at 15 nM, compared to effexors 35000 nM.

Which would explain why vortioxetines max dose is 20mg?
Compared to effexors 375 mg?
As the overall drug concentration of the latter can be pushed much higher??


Then, on vortioxetines wiki page, it has a follow on from Ki values,
 
[TABLE="width: 531"]
[TR]
[TD="width: 107"] Target
[/TD]
[TD="width: 58"] Affinity
[/TD]
[TD="width: 170, colspan: 2"] Functional activity
[/TD]
[TD="width: 180"] Pharmacodynamic action
[/TD]
[/TR]
[TR]
[TD="width: 58"] Ki (nM)
[/TD]
[TD="width: 115"] IC50 / EC50 (nM)
[/TD]
[TD="width: 51"] IA (%)
[/TD]
[/TR]
[TR]
[TD="width: 107"] SERT*
[/TD]
[TD="width: 58"] 1.6
[/TD]
[TD="width: 115"] 5.4
[/TD]
[TD="width: 51"] —
[/TD]
[TD="width: 180"] Inhibition
[/TD]
[/TR]
[TR]
[TD="width: 107"] NET*
[/TD]
[TD="width: 58"] 113
[/TD]
[TD="width: 115"] —
[/TD]
[TD="width: 51"] —
[/TD]
[TD="width: 180"] Inhibition
[/TD]
[/TR]
[TR]
[TD="width: 107"] 5-HT1A*
[/TD]
[TD="width: 58"] 15
[/TD]
[TD="width: 115"] 200
[/TD]
[TD="width: 51"] 96
[/TD]
[TD="width: 180"] Agonist
[/TD]
[/TR]
[TR]
[TD="width: 107"] 5-HT1B*
[/TD]
[TD="width: 58"] 33
[/TD]
[TD="width: 115"] 120
[/TD]
[TD="width: 51"] 55
[/TD]
[TD="width: 180"] Partial agonist
[/TD]
[/TR]
[TR]
[TD="width: 107"] 5-HT1D*
[/TD]
[TD="width: 58"] 54
[/TD]
[TD="width: 115"] 370
[/TD]
[TD="width: 51"] —
[/TD]
[TD="width: 180"] Antagonist
[/TD]
[/TR]
[TR]
[TD="width: 107"] 5-HT3*
[/TD]
[TD="width: 58"] 3.7
[/TD]
[TD="width: 115"] 12
[/TD]
[TD="width: 51"] —
[/TD]
[TD="width: 180"] Antagonist
[/TD]
[/TR]
[TR]
[TD="width: 107"] 5-HT7*
[/TD]
[TD="width: 58"] 19
[/TD]
[TD="width: 115"] 450
[/TD]
[TD="width: 51"] —
[/TD]
[TD="width: 180"] Antagonist
[/TD]
[/TR]
[TR]
[TD="width: 107"] β1-adrenoceptor
[/TD]
[TD="width: 58"] 46[6]
[/TD]
[TD="width: 115"] —
[/TD]
[TD="width: 51"] —
[/TD]
[TD="width: 180"] —
[/TD]
[/TR]
[/TABLE]
 
Functional activity - IC/EC50 values.

Under that heading - NET doesn't seem to feature, which would stand in contrast to the deduction made based on comparing it's Ki values to effexors.

So I suppose the question would be, to compare the IC/EC 50 values for the various drugs also - to determine their true binding profiles and receptor implications??

On that note - is there a page in wiki similar to the first link in this post, that outlines the "functional activity" for the various receptor subtypes for each drug??
 
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Something funny going on with site posting at the moment also...

Messages getting cropped and not posting fully.
 
Also trying to make sense of this.

Comparing duloxetine with venlafaxine in terms of NET.

The former at 5.9 nM/L
The latter at 2753 nM/L

If we were using the dose as being the drug concentration (which I'm assuming to do for now, as I don't know the actual means to determine the true concentration), then at a max dose of 60 mg cymbalta, 225 mg effexor:
Cymbalta roughly one quarter the concentration of effexor at full dose - that would still mean it's about 7x stronger in terms of NET implication.

So cymbalta would - by my ill-informed logic - have a much more potent effect on NET than effexor...

Yay or nay?
 
Affinities in the 3 uM range are not necessarily weak. You are thinking about affinity the wrong way. It is simply a measure of the concentration-dependence of binding. The way you are thinking about it is that "I've seen all these other drugs with high affinities in the nM range, and this drug has affinity in the uM, so it must be a weak drug."
Affinities are not evaluated like that. The Ki is simply a measure of what concentration produces 50% occupation.
 
serotonin2A said:
Affinities in the 3 uM range are not necessarily weak. You are thinking about affinity the wrong way. It is simply a measure of the concentration-dependence of binding. The way you are thinking about it is that "I've seen all these other drugs with high affinities in the nM range, and this drug has affinity in the uM, so it must be a weak drug."
Affinities are not evaluated like that. The Ki is simply a measure of what concentration produces 50% occupation.
Click to expand...

Okay then.

They're not evaluated like that.
Though many seem to claim that, by example, Ki value for 5HT2c blockade exhibited by agomelatine is 6000 nM - therefore this is a weak value...

Your contention is that this is not necessarily true.

So - how is the actual affinity/potency measured or evaluated?
 
JohnBoy2000 said:
Okay then.

They're not evaluated like that.
Though many seem to claim that, by example, Ki value for 5HT2c blockade exhibited by agomelatine is 6000 nM - therefore this is a weak value...

Your contention is that this is not necessarily true.

So - how is the actual affinity/potency measured or evaluated?
Click to expand...

I listed the criteria above:

1. What is the concentration of the drug at its site of action?
2. How selective is the drug?
3. How efficacious is the drug (what level of receptor occupation is required)?
 
I would have thought that drug affinities to receptors by Ki value is important for evaluating it's side effects & therapeutic effects.
For example;
Nortriptyline binds to SERT at 16.5nm. this makes it roughly, 16x weaker as an SSRI compared to something like, Sertraline.

Nortriptyline has the least side effects of the TCAs (Besides Tianeptine) due to it having weaker binding values to the mACH receptors.

Venlafaxine is entirely an SSRI at low dosages. As you increase the dose, the NRI effect becomes more prominent.

Seroquel, an antipsychotic, will only touch it's tightest binding receptor at low doses. Which is the H1 (Anti-histamine) so it is used as a sleeping pill at low doses, and it doesn't begin to become an anti psychotic until much higher does, where it begins to bind to Dopamine receptors, and 5ht2a.

Agomelatine, having only two doses, of 25mg & 50mg, will not be able to bind strongly to 5ht2c due to limitations on increasing doses.
Having used Agomelatine, it is very weak as an anti depressant vs something like Nortriptyline.
 
serotonin2A said:
I listed the criteria above:

1. What is the concentration of the drug at its site of action?
2. How selective is the drug?
3. How efficacious is the drug (what level of receptor occupation is required)?
Click to expand...

Alright - pardon me for being repetitive.
In fact, if you can link me a research paper of reference of some kind that explains the pure mechanics of binding affinity, that would probably be easiest.

In that absence of that however:

1) the concentration of the drug at site of action.
This is evaluated based on - drug dose? So like I mentioned, putting the Ki value in perspective of the mg dose the drug is being administered at.

2) How selective is the drug: In terms of the various receptors it binds to?

3) Drug efficacy - receptor occupation: This is ultimately the information I'm interested in, and I had assumed was dictated through the binding values.
Are you referring here to the Ki values?


Again - perhaps a slew of questions but, evaluating the drugs ultimate efficacy at a particular receptor, it's lack of effect on another receptor, appears to me at least to be a fairly complex topic - which will probably require a greater level of understanding than that which can be gleaned from a two or three line explanation.

Having a Ki of 631 nM doesn't necessarily mean that the effect is weak. Whether or not an affinity value is "weak" depends on a variety of factors.
1. What is the concentration of the drug at its site of action? If the typical concentration is 5 nM, then the affinity is low. However, if 500 nM is a typical concentration, then the situation is totally different.
2. How selective is the drug? If the drig has 10-fold lower affinity for all other sites, for example, then you can keep raising the dose until you see activity without inducing side effects.
3. For some effects, you may only need low levels of receptor occupation, so the Ki may be misleading.
Click to expand...


1) Take vortioxetine as an example.
How exactly are we being made aware what the "typical concentration" is??

[TABLE="class: wikitable"]
[TR]
[TD]Target[/TD]
[TD]Affinity[/TD]
[TD="colspan: 2"]Functional activity[/TD]
[TD]Pharmacodynamic action[/TD]
[/TR]
[TR]
[TD]Ki (nM)[/TD]
[TD]IC50 / EC50 (nM)[/TD]
[TD]IA (%)[/TD]
[/TR]
[TR]
[TD]SERT*[/TD]
[TD]1.6[/TD]
[TD]5.4[/TD]
[TD]—[/TD]
[TD]Inhibition[/TD]
[/TR]
[TR]
[TD]NET*[/TD]
[TD]113[/TD]
[TD]—[/TD]
[TD]—[/TD]
[TD]Inhibition[/TD]
[/TR]
[TR]
[TD]5-HT1A*[/TD]
[TD]15[/TD]
[TD]200[/TD]
[TD]96[/TD]
[TD]Agonist[/TD]
[/TR]
[TR]
[TD]5-HT1B*[/TD]
[TD]33[/TD]
[TD]120[/TD]
[TD]55[/TD]
[TD]Partial agonist[/TD]
[/TR]
[TR]
[TD]5-HT1D*[/TD]
[TD]54[/TD]
[TD]370[/TD]
[TD]—[/TD]
[TD]Antagonist[/TD]
[/TR]
[TR]
[TD]5-HT3*[/TD]
[TD]3.7[/TD]
[TD]12[/TD]
[TD]—[/TD]
[TD]Antagonist[/TD]
[/TR]
[TR]
[TD]5-HT7*[/TD]
[TD]19[/TD]
[TD]450[/TD]
[TD]—[/TD]
[TD]Antagonist[/TD]
[/TR]
[TR]
[TD]β1-adrenoceptor[/TD]
[TD]46[6][/TD]
[TD]—[/TD]
[TD]—[/TD]
[TD]—[/TD]
[/TR]
[/TABLE]
2) Okay - this one I think I get. Lesser Ki value at other sites, increase the dose and the the effect are the relevant receptor, without implicating the lesser valued receptors.

3) For some effects, only low level occupation is required.

Does this not allude to the potency of the drug?
By example - say, in terms of the not-so-well-informed, there's a neurochemical deficit of, noradrenaline.
The patients wish, is to correct this.
There, said patient would want a drug with high affinity for NET, alpha 2 blockade (antagonism or inverse agonism), and 5HT2c blockade (same effect) - the latter two implicating the potentiation of noradrenalines "presence"? It's effect, basically.

So given that that's the desired "effect" - what benefit would a lesser "occupation" be required?

Like I said - if you could direct me to a relevant wiki page or book chapter or research paper delineating this info - well, I'd appreciate a response regardless but, doing so would probably save us all time.
 
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