SAR (Ketoximes)

[dmitrij176]

In addition to SAR analysis that was posted in the wiki section (https://github.com/OpenSourceMycetoma/Series-6-Ketoximes/wiki/SAR-analysis-and-series-development), I would like to start a new issue where we can discuss future molecule planning for series 6.

In summary, it is mostly known what each motif (within the scaffold) role is, several factors remain to be decided upon.

1. Substrate selection. This field is always open for suggestions. We just sent our first batch of ketoximes to Erasmus MC for biological evaluation. Results from upcoming assays hopefully will clarify which structures to prioritise. Long hydrocarbon chains within the ketoxime moiety (like isopentyl) are the starting point and effects of cyclic structures are yet to be discovered. For commercially unavailable substrates, the issue can to be solved by making them via 3 step synthetic chain from accessible starting materials. Dimethylaminoethyl will be the first reagent made specifically to cover this need.
2. Main scaffold. While it is important to create a diverse library of ketoximes with the preserved original scaffold (2,4-diCl and pyridine configuration), its also worth considering alternative options which might improve physichochemical properties of the analogues. Two options exist here: changing one motif at a time or reshuffle an entire scaffold (eg: azole for N-heteroaromatic region and 2,4-difluoro phenyl ring). I would personally go for the second. Having analysed multiple papers, it seems that a lot of new generation molecules or already marketed drugs have triazole as the CYP51 heme binding moiety along with 2,4-difluoro substituted ring which is known to enhance lipophilicity (one of MycetOS main design criterion). Alternatively, totally new scaffolds bearing ketoxime group might be considered as well.
3. Linker region. Ketoxime lead has a CH2 linker. This can potentially be expanded to more carbon atoms (no more than 4), but it seems that one carbon group is enough to space out the interacting regions.
4. Separation of E/Z isomers. Research and discussion on this is still ongoing. Geometric isomers seem to be stable but prior to their separation, we need to ensure that they do not interconvert at rt. More information to follow. In case of separation, protocols have been prepared which would enable to shift equilibrium towards the preferred isomer. If the analogue is synthesised again, specific reaction protocols favouring one geometric form can be employed. Pyrifenox is an ideal candidate for E/Z separation. The molecule has performed well both in vitro and in vivo and has a MIC of 0.25 micromollar (as E/Z mixture). Inhibitory potential of separated forms might give more insight and direct future project work.

[bebi78]

@dmitrij176 @mattodd Maybe I missed it but what about the oxime component of oxiconazole? In terms of alternative scaffolds, I have deoxybenzoine and deoxyanisoine in my lab. If inactive, might show at least the importance of the pyridine ring.

[dmitrij176]

@dmitrij176 @mattodd Maybe I missed it but what about the oxime component of oxiconazole? In terms of alternative scaffolds, I have deoxybenzoine and deoxyanisoine in my lab. If inactive, might show at least the importance of the pyridine ring.

I think, it is generally a good idea to test as many different scaffolds as possible. The SAR section above is only a reflection of up to date work along with current findings. Therefore, I would consider new scaffolds for sure. For series 6 ketoximes, we havent yet tested compounds without pyridine ring, so for proof of concept purposes, suggested options would be interesting to evaluate.

[bebi78]

@dmitrij176 I can send you 2 or 3 grams of deoxybenzoine and deoxyanisoine if you want. I don't have alkylated hydroxyl amines here, and you are the expert with the synthesis. In terms of further azole motifs, maybe benzimidazoles (see project 5) and benzotriazoles would also be quite interesting.

[dmitrij176]

@dmitrij176 I can send you 2 or 3 grams of deoxybenzoine and deoxyanisoine if you want. I don't have alkylated hydroxyl amines here, and you are the expert with the synthesis. In terms of further azole motifs, maybe benzimidazoles (see project 5) and benzotriazoles would also be quite interesting.

That would be great. Substrates are not a problem at all. Can you send them then please.

[bebi78]

@dmitrij176 Sure. Can you give me your lab address and phone number? I will dispatch the package with the compounds by UPS on Friday.

[dmitrij176]

@dmitrij176 Sure. Can you give me your lab address and phone number? I will dispatch the package with the compounds by UPS on Friday.

UCL School of Pharmacy Dmitrij Melechov 29-39 Brunswick Square Bloomsbury WC1N 1AX London United Kingdom +447704713862

Thank you.

[dmitrij176]

@bebi78 could you please provide the SMILES for the scaffolds.

[bebi78]

@dmitrij176 Thanks. Here is the word file with the contents of the package including structures and SMILES codes.

Deoxyanisoin.docx

[bebi78]

@dmitrij176 Here is the UPS tracking number of the package. Estimated delivery is Monday morning. 1Z99F7F10494089905

[dmitrij176]

@dmitrij176 Here is the UPS tracking number of the package. Estimated delivery is Monday morning. 1Z99F7F10494089905

Thank you. Will let you know when delivered.

[dmitrij176]

@bebi78 your parcel has been delivered. Thank you very much.

O-methylhydroxylamine will be the substrate of choice for the 2 analogs.

[MFernflower]

@dmitrij176 I know you made a compound that was methylene shortened and had the chlorine removed but I don't think we made a compound where only the chlorine have been lopped off!

[dmitrij176]

@dmitrij176 I know you made a compound that was methylene shortened and had the chlorine removed but I don't think we made a compound where only the chlorine have been lopped off!

Removing halogen atoms from the scaffold will likely lead to loss of activity against the target. Besides, Ive just recently made 2 new molecules with deoxybenzoin and deoxyanisoin scaffolds. Lets see how they perform in the assay first.

[dmitrij176]

As part of Series 6 exploration, I came across oxiconazole which is currently the only marketed oxime type antifungal drug. The compound has not been previously biologically evaluated (Ive checked in the mycetoma database/spreadsheets) and I believe it needs testing against mycetoma (together with 2,4-diCl/2,4diF analogs which I am making). Oxiconazole is not expensive and can be purchased, but only as a nitrate formulation. @wwjvdsande would that formulation be suitable for the biological assay? @mattodd @bebi78 is there generally a synthetic approach to remove the nitrate? I was thinking of something similar to a acid-base work-up principle? Or maybe ion exchange (amberlyst)?

[bebi78]

@dmitrij176 Nitrate is often used as non-nucleophilic anion for azole drugs, maybe to increase the stability of these imidazolium compounds. So I would rather suggest that you also prepare nitrate salts of your most active ketoximes instead of forming the free base of oxiconazole. But you can try non-nucleophilic bases such as carbonates to prepare the free base if you want. Maybe it should be tested quickly then.

[dmitrij176]

@wwjvdsande @MA-Jjingyi I want to investigate ketoxime stability in buffer solution(s). For the in vitro tests is XTT the only buffer being used? Can you please advise me on this? Thank you in advance