'Insights Into Subtype Selectivity of Opioid Agonists by Ligand-Based and Structure-Based Methods' (DOI: 10.1007/s00894-010-0745-1) is the most practical introduction to the use of training-sets in the 3D-QSAR of ligands. In fact, I think that their are at least 2 other moieties for μ affinity that aren't common thus not spotted in this set. As it is, only position & direction of aromatic rings, positively ionizable functions, hydrogen-bond acceptors & hydrophobic parts of molecule & their relative positions are noted.
I believe that:
1)olefinic alkenes seem in allylprodine, 14-cinnamyloxycodeinone & 14-allyloxymetopon and a few others (the -C=C- of those three overlay, by the way)
2)and the second is a second ring aromatic that is some distance from the first. MOST of the potent opioids have 2 aromatics. The first seems to be limited to a benzene, phenol or a closely-matching 6-member aromatic (and a carboxamide is a bioisostere for a phenolic -OH) The second can be MANY 5-membered rings (6 ring aromatics not well studied or not active). YES the aromatic shows up, but isn't matched in this model.
One issue of 'Annual Report in Medicinal Chemistry' showed that along with 2-thiophene (thiofentanyl), a 2-furyl (furylfentanyl), a 2 thioazole (very potent it seems), oxazole, imidiazole and so on. It would appear that the altered potency is LogP. and rate of metabolism.
Now the important thing is that I just happened upon this paper and realized that even a clunky second PC running Linux can install CHARMM which is free. As ChemOffice users will know, finding minimum energy states is slow and imperfect. More than once I have had to start the MIC calculations with the compound 'altered' to avoid local minimum-energy states. Of course, their is some scope for positioning because most examples are only semi-rigid. It might take a whole weekend but if that PC was going to be sat there doing nothing than it's free (or almost) is it not? Now I had some help setting up all of that Linux stuff because I can only program in assembly language so several good friends did a lot for me. I did nothing except spot it's possible utility.
So now people can add their own designs and then seeing how well they do!
I really would love to see us using one of those free, Java programs that convert SMILES<--?IUPAC<--Image if only so we don't keep having to use 3rd party support for images. Of course, sekio is the real expert (thinking of you brother).
I do hope it is of value to people. I have another that compares the various DRI/NRIs (well, classes of stimulant) but as I am sure you know that an aromatic, a benzhydryl and an N: are the only requirements That said, an appropriate training set might tease out another moiety. There are a shed-load of smart people here so I am looking forward to being impressed.
-C-
PS I remain convinced that the p-Br analogue of BDPC (or C-8813) can be replaced with a -CH3 which as a lot of advantages. The more I look, the more I am convinced that 3-Amino-3-phenylpropionamide Derivatives ALSO have a decent (sub-nM) affinity IF they were tertiary amines. Put them next to each other! Now, I am not interested in the phenol-baring analogues as they often act as mixed agonist/antagonists but compound 4a with a dimethyl moiety (rather than a monomethyl) is worth looking into. The synthesis doesn't look THAT complex so I'm hoping SOMEONE is reading this. There are just SO MANY novel opioids.
I believe that:
1)olefinic alkenes seem in allylprodine, 14-cinnamyloxycodeinone & 14-allyloxymetopon and a few others (the -C=C- of those three overlay, by the way)
2)and the second is a second ring aromatic that is some distance from the first. MOST of the potent opioids have 2 aromatics. The first seems to be limited to a benzene, phenol or a closely-matching 6-member aromatic (and a carboxamide is a bioisostere for a phenolic -OH) The second can be MANY 5-membered rings (6 ring aromatics not well studied or not active). YES the aromatic shows up, but isn't matched in this model.
One issue of 'Annual Report in Medicinal Chemistry' showed that along with 2-thiophene (thiofentanyl), a 2-furyl (furylfentanyl), a 2 thioazole (very potent it seems), oxazole, imidiazole and so on. It would appear that the altered potency is LogP. and rate of metabolism.
Now the important thing is that I just happened upon this paper and realized that even a clunky second PC running Linux can install CHARMM which is free. As ChemOffice users will know, finding minimum energy states is slow and imperfect. More than once I have had to start the MIC calculations with the compound 'altered' to avoid local minimum-energy states. Of course, their is some scope for positioning because most examples are only semi-rigid. It might take a whole weekend but if that PC was going to be sat there doing nothing than it's free (or almost) is it not? Now I had some help setting up all of that Linux stuff because I can only program in assembly language so several good friends did a lot for me. I did nothing except spot it's possible utility.
So now people can add their own designs and then seeing how well they do!
I really would love to see us using one of those free, Java programs that convert SMILES<--?IUPAC<--Image if only so we don't keep having to use 3rd party support for images. Of course, sekio is the real expert (thinking of you brother).
I do hope it is of value to people. I have another that compares the various DRI/NRIs (well, classes of stimulant) but as I am sure you know that an aromatic, a benzhydryl and an N: are the only requirements That said, an appropriate training set might tease out another moiety. There are a shed-load of smart people here so I am looking forward to being impressed.
-C-
PS I remain convinced that the p-Br analogue of BDPC (or C-8813) can be replaced with a -CH3 which as a lot of advantages. The more I look, the more I am convinced that 3-Amino-3-phenylpropionamide Derivatives ALSO have a decent (sub-nM) affinity IF they were tertiary amines. Put them next to each other! Now, I am not interested in the phenol-baring analogues as they often act as mixed agonist/antagonists but compound 4a with a dimethyl moiety (rather than a monomethyl) is worth looking into. The synthesis doesn't look THAT complex so I'm hoping SOMEONE is reading this. There are just SO MANY novel opioids.
Last edited: