April 2018 Shipment for biological activity evaluation to Dundee #39
Comments
|
I think i found a mistake in the dataset? @maratsydney |
|
It is indeed unusual, I was aiming for the MK031-2a but apart from it isolated another product and with help of NMR was able to assign structure shown as MK031-2b. ELN entry |
|
Perhaps you had a mirrored impurity in your halogenated precursor? Any idea where it came from? |
|
@MFernflower I am sure that SM was pure and it's hard to imagine to have that mirrored precursor from the synthetic route that I was following to make it. *edited previous comment to add ELN entry |
|
It's a super-interesting compound @maratsydney has carefully isolated. At the moment we can only think that this implies some lability in the ether substituent. i.e. That it can, under certain conditions, be displaced and can then re-attach. But it needs more investigating if we're going to understand it. @mcoster |
|
@maratsydney Do you see any product where t-BuOH has displaced the Br? |
|
Hmm, interesting... Are you able to share the NMR data - what evidence shows that it is this particular regioisomer? @maratsydney |
|
Could it be? |
|
My thoughts exactly, @drc007 - it's easier to imagine a small amount of regioisomeric heteroaryl bromide escaping attention, than imagine a reasonable mechanism for the "mirrored" compound. If that phenethyl alcohol group were to depart, I would be leaning towards aryne type intermediates, but even then, why would that be regioselectively trapped back on the same carbon by pyrazole anion, and the bromide selectively displaced by the small amount of that alkoxide? |
|
@mcoster @maratsydney Might be difficult to distinguish by NMR? Is it a solid? Small molecule crystal structure. |
|
@drc007, @mcoster definitely crystal will be the best option. Now after you mentioned that isomer that I didn't consider before I got confused a bit again (need to look back at all NMR), but one of the non-direct evidences for proposed structure is coupling of protons on main heterocycle which appear when I nave nitrogen in north-west position (and J value is quite big 4-5 Hz) while in all other compounds these signals sharp singlets. And I imagine in proposed structure coupling between protons of main heterocycle looks impossible (just too far away from each other). See all the spectra for two compounds in attachment in MestreNova format. And talking about source of alcohol: when I was doing Buchwald-Hartwig reaction on the very same substrate I was able to get product with difluorophenylethanol sitting on both position, what suggest release of alcohol from degradation of the core at basic conditions. Later on I set up reaction with sodium tertbutoxide and difluorophenylethanol to verify that theory and it was successful. And one more comment on purity of starting material: I isolated about 7% of that isomer from reaction so it should be about the same amount of impurity in the SM but I don't see any additional peaks in NMR and on top of that SM was recrystallized after column. |
|
MK031-2a: 9.1 ppm seems quite far downfield for a pyrazine 1H signal - have you seen them this far downfield in other compounds? |
|
@mcoster Just checked that for starting material (with bromine on the RHS) it's 8.9 ppm, for compound with naked phenyl ring - 9.0 ppm, with 4-nitrophenyl 9.1. |
|
Interesting discussion and ideas here. @maratsydney I wonder if you can lay out the case (i.e. give us a pic of the NMR spectrum) for why we do not have the isomeric bromide present at the start of the displacement reaction. There is this issue of why sometimes we have singlets and sometimes doublets for the two protons attached to the pyrazine ring, but I'm pretty sure that's not related. |
|
@maratsydney - thanks for uploading the NMRs! I spent some time this morning poring over them, and I agree with you that it seems to be the transposed isomer, although a crystal structure would be fantastic. What a surprising result! It's interesting that no compound with pyrazole in both north-west and north-east is isolated. I wonder whether this chemistry could be optimised and then exploited to access analogues that are otherwise difficult to prepare?.. |
|
@mcoster thank you for spending time on NMR, always good to know that more experienced people support the same version. I am currently working towards getting crystals. And just to close that important point about the purity I attached NMR of that batch used in reaction. @mattodd good point that you mentioned about these doublets that we see sometimes. I will try to organize it nicely and will open another issue to ask about that interesting case, since all my attempts to find the answer were unsuccessful so far. |
|
Short but very important update: Apart from it I have got results of other x-ray samples that have doublets and they found to be connected the same way at the bottom of the core at position 8. Example below (NMR attached):
|
|
@maratsydney Looks like a nice short publication there ;-) |
|
Well now, that's interesting! Great work @maratsydney |
|
So do you think the displacement at the 8-position occurred when you introduced the difluorophenylethanol or as you have drawn it in the reaction above there was a rearrangement from the 5-positon to the 8-position when you introduced the pyrrazole? |
|
I wonder if the 8 position compound precursor (Let's just call it 8X) was formed during a rxn involving a reactive halogen (Marat's NBS experiments or during the production of the TP core as that requires use of iodanes - considering @david1597 might have made some 8X on accident) @mattodd @mcoster @MedChemProf ICP-OES would pickup if there is any iodine containing impurities in freshly cyclized TP core - but it's a destructive process and will only pickup iodine containing impurities as Cl and F exist on freshly made core |
|
It's a fascinating and important result. Three things:
|
|
Here are my thoughts on a plausible mechanism for formation of the unusual regioisomer, if it turns out to not be from a contaminant in the starting materials:
In the expected reaction pathway, the nucleophile attacks the ipso carbon, bearing the leaving group. With some nucleophiles, perhaps based on hard-soft properties, pKa's, reversibility, proton sources, phase of the moon ;) - attack para to the chlorine could give a Meisenheimer complex that is protonated, then deprotonated at a different position to give a new Meisenheimer complex, which loses chloride to give the unexpected regioisomer. (Notes: there are lots of resonance forms that could be drawn for the Meisenheimer complex, and where proton transfers occur, it is reasonable to invoke the nucleophile, ie. hydroxide/water, amine/ammonium salt, etc.) @maratsydney @david1597 @mattodd @Plebellec @CamilleHauguel Edit: at'ed relevant people |
|
Nice mechanism, @mcoster . I don't like the look of the carbanion (2nd structure, para addition) but that's a gut feeling rather than a rational one. Only one obvious resonance form without redrawing something exotic for the triazole ring. The final elimination could occur directly, right, without disturbing the aromaticity of the triazole. I'd have thought the ipso attack would be favoured by hard Nu, since the Cl will make the carbon more electron deficient than the para position, which would be attacked by softer Nu. That's what we're seeing I think, but early days. An experiment we talked about today is the control reaction without added nucleophile. Add to the list... |
|
I guess in the first step you park the anion on N7 then pick up the hydrogen at C5 to get to the same intermediate? Followed by simple elimination not involving triazole. You could also take MK031-2a and resubject to reaction conditions to see if MK031-2b is formed? |
|
Yes, N7 anion will certainly be major resonance contributor |
|
Potency data for the first run of the April batch has been received:
Once we have data from the second run (usually 7 days wait) I will repost and then update the wiki/master list/ELN/GH etc. We're still waiting on the Series 3 result, and that of the Pfizer re-run that was sent separately. Great to see two sets of potent compounds in this selection. |
|
@david1597 @mattodd Wonderful! I guess this allows the green light to tinker even more with the 2-(3-subsitutedphenyl)propan-1-ol series A few possible ideas: (edited to include last-min biphenyl and ring lock ideas based on the potency of OSM-S-532)
SMILES STRINGS: (X = S in tricyclic compound) Very interesting that the P-ethyl compound was active@maratsydney 4-tert-Butylphenylboronic acid is commercially available and so is 4-(Trimethylsilyl)phenylboronic acid *The precursor to my so-called 'firewalker' compound (bonus points if you get this reference)https://www.sigmaaldrich.com/catalog/product/aldrich/523674?lang=en®ion=AU - Firewalker |
|
FYI, here are the compounds we plan to send in the next shipment (potentially in the next 1-2 weeks). It may answer some questions about what happens next, esp regarding the Suzuki series.
Edited to fix a missing double bond in one of the structures |
|
@MFernflower It's usually a good idea to provide some rationale for your suggestions. It'll help when making decisions on what to synthesise next. (e.g. any particular reason for the tricyclic or biphenyl ideas?) |
|
@edwintse @david1597 The idea behind the biphenyl was because of the potency of the benzyl protected molecule (OSM-S-532) and the tricyclic is simply a ring lock of OSM-S-532 (edited main post to add this information in) |
|
How exciting! I would echo @MedChemProf 's suggestion in #49 that we need to keep our target compound profile in mind. There seem to be a number of recent structural changes that benefit potency, eg. benzylic OH, RHS indole/meta-aniline, meta-bezyloxy substituted LHS. However, we also need to keep in mind what these changes do to the ADME/DMPK properties. If we start a new issue in the near future to prioritise future directions, it would be really helpful to chart out the key structures, with not only the potency, but also cLogP and other key indicators. For example, the meta-benzyloxy LHS compund is interesting, but I presume it is higher logP, lower water solubility, etc? Might suggest priority should be given to exploration of the RHS indoles and indole isosteres. |
|
Agreed @mcoster - just commented in response to @MedChemProf at #49 (comment) The attractive aspect of the Pfizer and indole/meta-NH2 compounds is that the potency is achieved through the addition of polar groups. I've not calculated, but I'm assuming the cLogPs are good, and we need to maintain this trend for all future compounds here. @MedChemProf proposed benzylic amines, for example, are great and maintain the other polar groups. Also avoiding metabolically labile groups (or toxic) groups is then the remaining item on the checklist. |
|
Agreed @mcoster @MedChemProf @mattodd. I think we're at a good point to take a step back and look at the big picture of where we are, and where we need to be with respect to properties other than potency. Let's wait till we have the second run back from Dundee and then kick off that discussion in more detail. @MFernflower With the 2-phenylpropan-1-ol series, this was the series I was heavily focused on earlier in the year but then paused as it became evident the original Pfizer hit was the OHOH compound and they became the priority. I still have some of these 2-phenylpropan-1-ol compounds to finish off (including anilines that can be acetylated) that are at varying stages of completeness, although it's unlikely I'll get this done within the next two weeks with the current focus on trying to get a 5-substituted amine. |
|
@david1597 @mattodd Indeed - all focus should be put into the palladium coupling and other steps needed to get the 5-phenethylamino compound but I do feel at some point we should combine the things we have learned about the RHS and LHS into a single molecule (Addressing the rather polar elephant in the room so to speak)
|
|
One thing to bear in mind if the meta-amino substituted compounds are explored further - many anilines have nasty metabolites, including mutagenic properties. Here's a paper from AZ where they looked at getting rid of mutagenicity in aminobiphenyls (admittedly, the para-substituted ones, though). They have some interesting observations around putting a fluorine or chlorine meta to the amine, so it is also ortho- to the other aryl group - there's an interesting interplay between the inductive effect of the halogen and the conformational change around the biaryl bond. The above, and looking at the 3D models we made at GU as trophies for undergrad prizes has me wondering about substitution at this position of the RHS substituent. I can't recall having seen this explored in the compounds tested previously? Changing the orientation of the RHS substituent relative to the triazolopyrazine core could have an interesting influence on the activity, particularly if there is a H-bonding group, eg. indoles, meta-amines.
|
|
A few thoughts. Some very interesting results but perhaps we need to get repeats before embarking on long syntheses ;-) |
|
Yes indeed - we need to wait for the repeats from Dundee (usually 7 days) and the usual thing (hopefully this batch is the same, otherwise we'll chase) is to secure cytotox data on actives. |
|
@drc007 Typo. I've edited the original to fix it. Thanks |
|
@drc007 that "virtual ring" idea is interesting - the fluoro analogue on @david1597 's list will be interesting. Biphenyl itself has a 'twist angle' of about 45 degrees. If you put halogens in the 2 and 2' positions, it goes to ~ 60 (F) then to almost 90 degrees (Br and I).Ref Since the Series 4 compounds generally have no ortho substituent on the RHS aryl substituent, and the biaryl bond links to a 5-membered ring, where one of the adjacent atoms is a nitrogen, I wouldn't be surprised if the twist angle is less than 45 degrees. I think atropisomers would be a possibility if we had two ortho substituents on the RHS aryl group, ie. X,Y ≠ H. But, I think if we had only one ortho subsituent (eg. X = Cl, Y = H), we would still have relatively free rotation with the X group going past the triazole nitrogen. |
|
I do agree that it is time to move away from the aminobenzene subunits and stick to indole like ring systems (because of fears of idiosyncratic hepatotoxicity - I think it would be important to stop making aminobenzenes after the compound needed (ortho-methyl) to test the virtual indole theory ) - As a matter of fact
I seem to remember proposing a benzofurazan compound but the boronic acid
for it was like 200 AUD
<br>
Benzimidazole 5 boronic acid is commercially available so it seems like a logical next step onwards from the indole hit?
@david1597 @mcoster @maratsydney
(Sorry about all the edits - I really really had to think this post through}
|
|
@maratsydney Are the crystal structure files for MK031-2a available? Would be interesting to look at the angle between the rings. @mcoster @MFernflower I think you mean benzofuran, might be interesting to compare a compound without an N-H but electron-rich heterocycles are often good substrates for CYP450 enzymes. Benzimidazole would also be interesting, as would the various azaindoles but some would require synthesis of the appropriate boronic acids. |
|
The benzimidazole boronic acid can be grabbed from sigma
https://www.sigmaaldrich.com/catalog/product/aldrich/cds024320?lang=en®ion=US
@drc007
^ I think this should be a semi-priority compound to make @maratsydney @david1597
also Dr.Swain I was referring to benzofurazan - a little known heterocycle that has interesting properties but would probably be shredded by the CYP system
(example paper https://www.researchgate.net/publication/262230240_Benzofurazan_derivatives_as_antifungal_agents_against_phytopathogenic_fungi )
|
|
Please ignore the previous comment I made @maratsydney @drc007 @david1597 - I had erroneously thought the indole ring was linked to the TP core at posistion C5!!!! I was wrong - it's C6 Some relevant boronic acids linked at that position are commercially available: https://www.sigmaaldrich.com/catalog/product/aldrich/708631?lang=en®ion=AU https://www.sigmaaldrich.com/catalog/product/aldrich/702188?lang=en®ion=AU (benzimidazole precursor - this will need to be subjected to Miyaura Borylation) - See this paper for interesting variant of the reaction https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3994125/ https://www.sigmaaldrich.com/catalog/product/aldrich/cds019261?lang=en®ion=AU https://www.sigmaaldrich.com/catalog/product/aldrich/cds024473?lang=en®ion=AU |
|
@drc007, I posted all xray files that I have with the structures in #46. @MFernflower benzimidazole is worth to try and I believe that two nitrogens in benzimidazole ring should be equivalent (and a real structure something average) - so it doesn't matter if it's position 5 or 6. This is my opinion, would love to hear confirmation. |
|
That might be a question @mcoster can answer |
|
I'm sure many can answer! They're tautomers and not quite equivalent, since one nitrogen is para- and one meta- to the attachment point, but I suspect they would be very similar in energy and rapidly interconverting, and hence shouldn't make much difference whether it is 5- or 6- position. |
|
@mcoster Believe it or not I actually did not realize until you mentioned it that benzimidazole tautomerizes |
|
@maratsydney alongside the benzimidazole I would be curious to see what the homologous quinoline compound would fair in terms of potency since it has no N-H bond https://www.sigmaaldrich.com/catalog/product/aldrich/641618?lang=en®ion=AU Once again this is pricey but still could be worth a try Edit: I don't think the nitrogen atom of that boronic acid aligns with the N of the indole - Quinoxaline is a better match but is really pricey for the 6 boronic acid https://www.sigmaaldrich.com/catalog/product/aldrich/708631?lang=en®ion=AU |
|
Second run of data has been received and is these results are in a new issue - #56. This issue must now be one of our longest in terms of number of comments! I'll try and tidy it up - separate out the various discussions into new issues if needed - and then this one can subsequently be closed. |
Update 25/7/18: Second run data has been received - link
OSM group in Sydney decided that there is no better way to celebrate Malaria day than send new batch of compounds for evaluation! Who knows, maybe the key molecule for the victory over Malaria now sitting in queue for the plane to UK.
The second batch of compounds for year (shown below) have now been shipped to Dundee for screening against P. falciparum.
2018.04.24 Dundee.cdx.zip
The text was updated successfully, but these errors were encountered: