• N&PD Moderators: Skorpio | thegreenhand

Bicyclic dimethylarylamine opioids - I need more for training set. Help please?

clubcard

Bluelighter
Joined
Apr 12, 2013
Messages
1,483
I'm sure that anyone with a keen interest will own a copy of 'Opiates' by Lenz et al. Page 441, section D. 'Benzylamine-Based Compounds'. 5-(dimethylamino)-4,4-dimethyl-1,5-diphenylpentan-1-one is listed as equipotent with codeine. What is of vastly more interest is the fact that it's structure is midway between BDPC (and I assume C-8813) and the 3-Amino-3-phenylpropionamide class. Ciramadol may be considered the lead compound and so my first question is, do people think that this scaffold is chiral? It's important to grasp how important the phenol (or bioisostere of same) is. I don't believe it's possible to produce an antagonist without a phenol (for example). One epimer of Alvimopan, meptazinol & picenadol all display agonism (sometimes silent agonism) while another is an antagonist. What they all display is a dearth of useful data when used in a training set.

The dimethyl moiety (or biostere) should be familiar from some very old opioids (like 3,3-dimethylpethidine, 3,3-dimethylprodine dimethylaminopivalophenone, 3,3-dimethylpropiram) but as you can see from the image, it is a key moiety but like the alkene (allylprodine, cinnamyloxycodone), no software deals with it. What IS important is that wherever a chiral methyl (typically) moiety is present, in every case pethidine to fentanyl, the 3,3-dimethyl is as potent (per mol) as the if having a slightly higher MW (due to extra -CH2). Anyone who has studied the Eunoia disc will be aware that derivatives of propiram, phenapromide & diampromide all perfectly overlay fentanyl. There is no bulk preventing the dimethyl (or indeed a -CH3 & -OH at the 3 position were found to be active) from binding... it just means 2 isomers, not 4.

So I post this just to see if others can further evolve a QSAR for the class. The benzyl amine is the BIG difference. As people may be aware, Dr. Lednicer first made pethidine-like compounds with a 4-piperidone aromatic with the benzyl dimethylamine and was rather surprised. I does however seem like others have stumbled upon the same things. Compound 82 may benefit from a p-NO2 on the benzophenone moiety and I'm pretty sure a dimethyl on the phenylethyl propanamide class (Itself brushing the benzamide opioids like U-47000). We know that a 2-(2-thienyl)ethyl moiety (see C 8813) increases potency by almost exactly the same % as thiofentanil is from fentanyl. That being the case, Jansen's exhaustive experiments on that ethylaryl moiety uncovered the fact that an N-2-(1,3-thiazole)ethyl moiety produces a compound some x4 of it's parents but also a duration x4 of it's parent.

Sorry to ramble on but if there are compounds you think should be added, please let me know - it's all going into a training set (and everyone will have access).

https://imgur.com/a/XnqoVho



PS I vaguely remember a weak (400mg = 8mg codeine) opioid which was an N,N-dimethyl-1-phenyl-1-pyridinyl)methanamine. I forget where the N went and the search engine sucks. Can anyone identify it as it neatly links propiram to the others.
 
And being the idiot I am, I forgot to mention lefetamine. The one's whose structure eluded me was doxpicopamine.

https://imgur.com/a/LdUxSns

Just the optical resolution would explain SO MUCH. But we also bear in mind that the Straub test is notoriously unreliable. I've also taken a keen look at the PEA class of opioids (lefetamine being the prototype). A bit of rummaging gives everyone the chance to fire up Chemoffice and perform the overlay calculations. I haven't posted the reversed ester of nortilidine (a cyclopentane, not cyclohexene) because I'm patenting a 2-step enanthiomerpure synthesis but the Wiki page on (nor)tilidine links to ehe original (awful) route. That the (1S,2R) isomer is an opioid while the (1R,2S) isomer is an NMDA antagonist is interesting. a DRI to offset this would be a bonus. What is important is that cemfentamine has noticeable opioid activity, has quite a lot of bulk considering it's MW and in all cases, it's the secondary, not tertiary amine that is active (in spite of reports, the dinor isn't active in man). Now here's the key part. Camfentamine overlays a crucial part of etorphine. In spite of it having no O lone-pairs to bind with, it's still active. Once yo do those minimum-energy calculations, you will see why the secondary is active.... and why neither the tertiary nor the primary are active (overlay the N: and it becomes clear).

So, if people paid attention to the QSAR of isopethidine (for example) and noticed that ethyl 1-methyl-3-(2-methylphenyl)piperidine-3-carboxylate (an o-tolyl rather than a benzene!), an isopethidine derivative, is as potent as pethidine. My conjecture is that like the other PEA opioids, the amine & aromatic are in the right spacial relationship hence other moieties not required for affinity. That o-tolyl? Well it's important in keeping the potency (some x4 pethidine). I have seen a couple of patents that used amino-acid residues as opioids and their benzenes always had a 2,6-dimethyl (meta xylyl) motif. Without it, you fall off an activity cliff. So I propose that the ring-substitution is to remove axial rotation of the aromatic ring. In short, it lowers that Ki and in some examples, sub-nm was recorded (again, don't trust just 1 set of figures.

Final note. Etonitazene is x60M. However, the addition of a 2S carboxamide (-CONH2) on that methyl spacer increases potency by a factor of 8. German researchers tested the racemate but a decent training set showed that the non-basic N (so N:) overlays the N in the chiral MCOPPB,NNC 63-0532 scaffolds and with O: in a number of other NOP ligands. I appreciate it IS a guess but we have very good training sets for MOP,DOP & SOP but nothing nearly as good for NOP. Evidence is turning up that NOP/DOP interaction can increase analgesia without leading to respiratory depression (previously the drug-of-last-resort was an opioid/NMDA agent) but it seems to be the case that MOP/NOP interaction decreases the dose needed for white mice to bend their tails into an S shape... and the microtomes.

https://imgur.com/a/Ww0EhJJ0
 
Ciramadol may be considered the lead compound and so my first question is, do people think that this scaffold is chiral?

The scaffold where the carbon alpha to the nitrogen is tertiary is certainly chiral. The "phenolic derivative of BDPC investigated by Dr. Daniel Lednicer" - where the carbon alpha to the nitrogen is quaternary and two of its substituents are identical - is, however, achiral.

For your training set, there is a series of compounds from Pfizer (https://doi.org/10.1016/S0960-894X(00)00034-2) which fit the class. I see that you posted one of these structures, so my apologies if you already had the full series.
 
The scaffold where the carbon alpha to the nitrogen is tertiary is certainly chiral. The "phenolic derivative of BDPC investigated by Dr. Daniel Lednicer" - where the carbon alpha to the nitrogen is quaternary and two of its substituents are identical - is, however, achiral.

For your training set, there is a series of compounds from Pfizer (https://doi.org/10.1016/S0960-894X(00)00034-2) which fit the class. I see that you posted one of these structures, so my apologies if you already had the full series.

I'm after compounds I haven't already listed - I need 20 or so. I just hoped someone had spotted examples. 1 of example has geometric isomerism (i.e. it isn't achiral, you sre mistaken)) doesn't harm the training-set. You don't pick the 20 most potent examples, you pick a set with varying affinity - I'm choosing the benzylamines.
 
Last edited:
1 of example has geometric isomerism (i.e. it isn't achiral, you sre mistaken)) doesn't harm the training-set.

The molecule as drawn has a mirror plane right down the centre, between the two quaternary carbons of the cyclohexane. This necessarily makes it achiral. The fact that two or more geometric isomers of a compound can exist does not mean that the compound is necessarily chiral.
 
The molecule as drawn has a mirror plane right down the centre, between the two quaternary carbons of the cyclohexane. This necessarily makes it achiral. The fact that two or more geometric isomers of a compound can exist does not mean that the compound is necessarily chiral.

I'm afraid to NEED to point this out but geometric isomerism is a key element of medicinal chemistry and you aren't going to be able to convert between the Z & E isomers of BDPC, for example. The class is usually taught using an alkene which is VERY common indeed.
 
I'm afraid to NEED to point this out but geometric isomerism is a key element of medicinal chemistry and you aren't going to be able to convert between the Z & E isomers of BDPC, for example. The class is usually taught using an alkene which is VERY common indeed.

A molecule is, by definition, chiral if it is non-superposable on its mirror image. When a molecule has a mirror plane, it will necessarily be superposable on its mirror image, and therefore achiral. The molecule discussed above has a mirror plane, as does BDPC - therefore, they are both achiral. This is not related to the presence of geometric isomers. Take, for example, 2-butene. It exists as two geometric isomers, cis-2-butene and trans-2-butene. Both of these molecules are completely planar; therefore, they are both superposable on their mirror images and both achiral.
 
So please explain helicine - just another of the many forms of isomerism. I this case, molecular overcrowding. Geometric isomerism, for example, is displayed in helicine or as I pointed out, E/Z isomerism (e.g. alkene). For the hard of thinking - cinnamyl groups are OBVIOUSLY non-interchangable.

If you can only manage to visualize a molecule in 2D, I regret to tell you that they exist in 3D. As for atropisomerism, I don't know how to explain it since it's a 3D form.

If you have anything useful to add to the set then please go ahead. If you simply want to argue the toss because YOU can't understand it, please leave it to those of us who can.
 
So please explain helicine - just another of the many forms of isomerism. I this case, molecular overcrowding. Geometric isomerism, for example, is displayed in helicine or as I pointed out, E/Z isomerism (e.g. alkene). For the hard of thinking - cinnamyl groups are OBVIOUSLY non-interchangable.

If you can only manage to visualize a molecule in 2D, I regret to tell you that they exist in 3D. As for atropisomerism, I don't know how to explain it since it's a 3D form.

Chiral helicines exist in two non-superposable mirror-image forms that cannot interconvert easily due to a high barrier to rotation. This is also the case with compounds that display atropisomerism: if you take the two enantiomers of a chiral atropisomeric compound, they are mirror images of each other, and they do not superpose.
 
Chiral helicines exist in two non-superposable mirror-image forms that cannot interconvert easily due to a high barrier to rotation. This is also the case with compounds that display atropisomerism: if you take the two enantiomers of a chiral atropisomeric compound, they are mirror images of each other, and they do not superpose.

Do you mean like the energy barrier in BDPC swapping from cis to trans? Diasteromers which begat trans/cis as well as conformers and rotamers & ligand isomerism. About the simplest example of cyclohexane (for example) which will will adopt chair conformation to reduce ring-strain but will adopt half-chair, boat, and twist-boat conformers depending on substitution. You cannot just use a mirror to describe isomerism. When lone-pairs define isomerism, how exactly do you see that in a mirror? Isomerism occurs even in compounds without a single carbon in sight. If you want to delve deeper, D is sometimes purposefully substituted for H to provide asymmetry in achiral compounds. Of course, BDPC isn't achiral as I have explained 3 times....
 
You cannot just use a mirror to describe isomerism. When lone-pairs define isomerism, how exactly do you see that in a mirror? Isomerism occurs even in compounds without a single carbon in sight. If you want to delve deeper, D is sometimes purposefully substituted for H to provide asymmetry in achiral compounds. Of course, BDPC isn't achiral as I have explained 3 times....

This is the definition of chirality from IUPAC:

chirality

The geometric property of a rigid object (or spatial arrangement of points or atoms) of being non-superposable on its mirror image; such an object has no symmetry elements of the second kind (a mirror plane, σ = S1, a centre of inversion, i = S2, a rotation-reflection axis, S2n). If the object is superposable on its mirror image the object is described as being achiral.

BDPC has a mirror plane and is therefore achiral. I think the disconnect here is that you are using "chiral" as a general term for compounds which display stereoisomerism, when in fact it is a specific type of stereoisomerism. Chiral compounds come as pairs of enantiomers, each of which has an equal and opposite ability to rotate plane-polarized light. The two stereoisomers of BDPC are diastereomers, not enantiomers; neither of them has any optical activity.
 
This is the definition of chirality from IUPAC:



BDPC has a mirror plane and is therefore achiral. I think the disconnect here is that you are using "chiral" as a general term for compounds which display stereoisomerism, when in fact it is a specific type of stereoisomerism. Chiral compounds come as pairs of enantiomers, each of which has an equal and opposite ability to rotate plane-polarized light. The two stereoisomers of BDPC are diastereomers, not enantiomers; neither of them has any optical activity.

Whatever you say - cis BDPC is inactive, trans BDPC is active.

Is this some need to prove you have read a few books? I'm looking for a training set (you still seem unable to add to) and the dunning-kruger effect means you can't even build a dreiding model? Can you just leave it to people who might have some USEFUL input. Sorry to sound so negative but I'm looking for candidates. Trans & cis BDPC are UTTERLY different and don't interconveine. If, after all this you can't deign to add one, it does look rather like someone keen to show off rather than add to the sum knowledge of the subject?

Sorry to sound so negative but you are determined to argue in a public space so a few home-truths in the public space are close. I really don't want to do that bot because you aren't worth it, but because any real chemist already KNOWS exactly what is being said. Sticking your hand up and pleading 'please sir!' at every juncture does tend to re-enforce the notion that sekio was snowed under and nobody wanted the job... I mean, 7th choice? No exactly a vote of confidence is it? So surprise me - submit a compound. I just throw it into CHARMM so there is no opinion of it's usage....

But really, have some self respect; you aren't garnering respect off anyone else so you need to start somewhere.

Sorry to be brutal - but better me than a dozen poor cunts you bully.
 
Whatever you say - cis BDPC is inactive, trans BDPC is active.

Is this some need to prove you have read a few books? I'm looking for a training set (you still seem unable to add to) and the dunning-kruger effect means you can't even build a dreiding model? Can you just leave it to people who might have some USEFUL input. Sorry to sound so negative but I'm looking for candidates. Trans & cis BDPC are UTTERLY different and don't interconveine. If, after all this you can't deign to add one, it does look rather like someone keen to show off rather than add to the sum knowledge of the subject?

Sorry to sound so negative but you are determined to argue in a public space so a few home-truths in the public space are close. I really don't want to do that bot because you aren't worth it, but because any real chemist already KNOWS exactly what is being said. Sticking your hand up and pleading 'please sir!' at every juncture does tend to re-enforce the notion that sekio was snowed under and nobody wanted the job... I mean, 7th choice? No exactly a vote of confidence is it? So surprise me - submit a compound. I just throw it into CHARMM so there is no opinion of it's usage....

But really, have some self respect; you aren't garnering respect off anyone else so you need to start somewhere.

Sorry to be brutal - but better me than a dozen poor cunts you bully.

Clubcard, please refrain from personal attacks and rudeness. I have done nothing but respectfully explain why the compound you posted is achiral after you stated that "[I was] mistaken" in making that claim.
 
Last edited:
The ketamine molecule also has a structure where there's an amino group at a carbon that is directly connected to an aromatic ring. But there's only one n-methyl. Ketamine is known to bind to the opioid receptors with a low affinity, so it may also be interesting in a molecular docking simulation.
 
Well, if people work backwards from the Upjohn BDPC stuff, they will see the simpler cyclohexanone opioids themselves derived from some of the PCP analogues. Upjohn spent a good 12 years and went through about 1200 compounds so while DL doesn't have access to his old notebooks, he was able to talk through the rational design process.
 
J. Med. Chem.; 1985 Dec; 28(12) 1947-9 has the appropriate citations. Casy exhaustively studied the pethidine & prodine scaffold so worth reading it all.
 
https://doi.org/10.1111/j.2042-7158.1968.tb09636.x - 1‐Allyl and 1‐(3, 3‐dimethylallyl) analogues of pethidine and its reversed esters

It's also worth looking at the propiram & phenapromide. You will note that they share a piperidine ring in their basic nitrogen & that the 3,3-dimethyl derivatives of those are some 6-8x more potent. Od course, a 4-phenyl produces a compound some x60 morphine since it then overlays fentanyl and I would guess other aromatics would work similarly. They key point is that the 3,3-dimethyl moiety works best when it is achiral as it would be in 3,3-dimethyl fentanyl. I cannot remember the patent but I believe it's a 1970s BOC one one 3-methyl-3-hydroxy fentanyl that proved to be more active than fentanyl.
 
BDPC has a mirror plane and is therefore achiral.

that's news to me. Like all other 1,4 substituted cyclohexanes BDPC is a chiral compound with 2 chiral centres and 4 possible configurations (+)/(-)-cis/trans. You can have both the hydroxy and the amine equatorial (one trans isomer), the hydroxy equatorial and the amine axial (one cis isomer), the hydroxy axial and the amine equatorial, (another cis isomer), or both hydroxy and amine axial (another trans isomer).

4 images of each isomer for your viewing pleasure:
NSFW:

(OH eq, NMe₂ ax)
BBgnEes.png

(OH ax, NMe₂ eq)
9Mw3Siq.png

(OH eq, NMe₂ eq)
V0HEEHb.png

(OH ax, NMe₂ ax)
ykJQNxQ.png

 
Top