OpenSourceMycetoma / Series-2-Aminothiazoles

Series 2
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Resynthesis of MMV006357 #4

Closed kym834 closed 3 years ago

kym834 commented 4 years ago

Hi @bendndi @drc007 @wwjvdsande,

I've had a look at the synthesis of MMV006357 and would be happy to resynthesis it here at The University of Sydney and ship to @wwjvdsande & co. so that the activity can be confirmed and kick off this series. Is there still an interest in pursuing it?

I was also wondering, in regard to doing some synthesis for a SAR study, would the activity need to be confirmed in vitro and in vivo before we set about synthesising some analogues in which case we would have to wait until the northern hemisphere summer for in vivo testing results? Or, would activity confirmation in vitro be enough that we could start exploring the synthesis of analogues sooner?

wwjvdsande commented 4 years ago

Hi @kym834 @bendndi @drc007, MMV006357, MMV675968 and MMV022478 all had potent in vitro and in vivo activity. In the larvae model they performed well. For these compounds the in vivo activity has therefore been proven and in my opinion they would be good starting points for new compound series. If you would willing to make a series out of MMV006357 we could certainly screen in in vitro in the wintertime and than start testing in vivo when the spring comes.

bendndi commented 4 years ago

@kym834 I think it could be great to resynthesize a batch of 006357 and perhaps make a handful of close analogues at the same time. If you make some suggestion on a set of analogues I'm happy to chime in and help prioritize / enhance the list. The easiest way to track would be to have a SMILES list of structure ideas somewhere, but if that's not possible a chemdraw picture would work in the first instance. I would not worry about the timing of the synthesis relative to the assays, compounds can always just sit in a fridge waiting for the assay to be avaialble.

drc007 commented 4 years ago

@wwjvdsande @bendndi @kym834 A lot of aminothiazoles are commercially available, whilst it would be very useful to have a fresh supply of MMV006357 available and retested, perhaps we can scope out the SAR with commercial samples?

https://github.com/OpenSourceMycetoma/Series-2-Aminothiazoles/issues/2

MFernflower commented 4 years ago

https://www.frontiersin.org/articles/10.3389/fmicb.2018.02542/full

@drc007 @bendndi

Aminothiazoles are thought to work via inhibition of aerobic respiration

this does not discount the possible uses of this compound (E.G azoxystrobin causes ATP levels to plummet but is rather safe) but animal cell tox might need to be watched out for

MFernflower commented 4 years ago

@kym834 @drc007 I agree it would be wise to make a few simplified analogues of this compound - N,4‐diphenyl‐1,3‐thiazol‐2‐amine to me sounds like an easy one to bang out!

MFernflower commented 4 years ago

@wwjvdsande @bendndi @Wilson-Lm @mattodd While we cannot yet confirm the MOA of the aminothiazole as being a succinate dehydrogenase inhibitor or perhaps a glycolysis inhibitor - is there any data of commercial SDHI's (boscalid, carboxin, benodanil or flutolanil) vs Madurella mycetomatis?

wwjvdsande commented 4 years ago

@MFernflower not than I'm aware of

bendndi commented 4 years ago

Here are some ideas for very close scan analogues around MMV006357: image

And same as SMILES:

SMILES Tag
Cc1ccnc(Nc2nc(cs2)c3ccccn3)c1 MMV006357
Cc1ccnc(Nc2nc(cs2)c3ccccc3)c1 AT_BP_001
Cc1ccnc(Nc2nc(cs2)c3ccncc3)c1 AT_BP_002
Cc1ccnc(Nc2nc(cs2)c3cccnc3)c1 AT_BP_003
N(c1ccccn1)c2nc(cs2)c3ccccn3 AT_BP_004
Cc1cccc(Nc2nc(cs2)c3ccccn3)c1 AT_BP_005
Cc1ccnc(Nc2ncc(s2)c3ccccn3)c1 AT_BP_006
Cc1ccnc(Nc2nc(cs2)c3ccccc3F)c1 AT_BP_007
Cc1ccnc(Nc2nc(cs2)c3ccc(Cl)cc3)c1 AT_BP_008
COc1ccc(cc1)c2csc(Nc3cc(C)ccn3)n2 AT_BP_009
Fc1ccccc1Nc2nc(cs2)c3ccccn3 AT_BP_010
C(Nc1nc(cs1)c2ccccn2)c3ccccn3 AT_BP_011
O=C(Nc1nc(cs1)c2ccccn2)c3ccccc3 AT_BP_012
drc007 commented 4 years ago

As might be expected most of these aminothiazoles are known compounds, I've added the InChiKey and searched a variety of online databases

SMILES Tag InChIKey ChEMBL ZINC eMolecules Mcule MolPort
Cc1ccnc(Nc2nc(cs2)c3ccccn3)c1 MMV006357 QMEBVRXZLKAAIG-UHFFFAOYSA-N CHEMBL476339 ZINC000000088330 1509070 MCULE-5313198933 MolPort-002-013-562
Cc1ccnc(Nc2nc(cs2)c3ccccc3)c1 AT_BP_001 YIJMAUFKBCAMPF-UHFFFAOYSA-N CHEMBL1622956 ZINC000000190240 1321658 MCULE-3588516968 MolPort-001-958-994
Cc1ccnc(Nc2nc(cs2)c3ccncc3)c1 AT_BP_002 QONSPCMVAHVLGB-UHFFFAOYSA-N CHEMBL3321862 ZINC000000088501 1509148 MCULE-9214113868 MolPort-000-690-546
Cc1ccnc(Nc2nc(cs2)c3cccnc3)c1 AT_BP_003 JPOFCGIZOBPUSQ-UHFFFAOYSA-N ZINC000000088711 1509104 MCULE-4995452320 MolPort-000-690-559
N(c1ccccn1)c2nc(cs2)c3ccccn3 AT_BP_004 RYCUBTFYRLAMFA-UHFFFAOYSA-N CHEMBL489770 ZINC000000257247 1284347 MolPort-000-006-123
Cc1cccc(Nc2nc(cs2)c3ccccn3)c1 AT_BP_005 DQQQXXNDHIYTLC-UHFFFAOYSA-N CHEMBL567008 ZINC000000088164 1260877 MCULE-7011722160 MolPort-000-690-520
Cc1ccnc(Nc2ncc(s2)c3ccccn3)c1 AT_BP_006 GAAZWVOHHYHPRR-UHFFFAOYSA-N
Cc1ccnc(Nc2nc(cs2)c3ccccc3F)c1 AT_BP_007 CXMUWUHCBOUUOJ-UHFFFAOYSA-N
Cc1ccnc(Nc2nc(cs2)c3ccc(Cl)cc3)c1 AT_BP_008 SBWIYNYNJAKRHN-UHFFFAOYSA-N CHEMBL530636 ZINC000000246761 1321660 MCULE-1723642500 MolPort-001-958-995
COc1ccc(cc1)c2csc(Nc3cc(C)ccn3)n2 AT_BP_009 LOFZQPZBTLGLOP-UHFFFAOYSA-N CHEMBL4096214 ZINC000004117008 1321662 MCULE-4324912730 MolPort-000-690-731
Fc1ccccc1Nc2nc(cs2)c3ccccn3 AT_BP_010 VVSAPVJXTYIRNE-UHFFFAOYSA-N CHEMBL2441361 ZINC000000813402 1509050 MCULE-1162352817 MolPort-002-013-555
C(Nc1nc(cs1)c2ccccn2)c3ccccn3 AT_BP_011 LLANOFYTSFTNJV-UHFFFAOYSA-N
O=C(Nc1nc(cs1)c2ccccn2)c3ccccc3 AT_BP_012 NNBHDRDMPNNEKO-UHFFFAOYSA-N CHEMBL164087 MolPort-004-132-922
drc007 commented 4 years ago

Hi @bendndi @kym834 @mattodd Given that aminothiazoles are so common perhaps we should look to "crowd source" compounds. Put out a call for people/vendors to search their catalogues/ compound collections and donate a couple of compounds each?

bendndi commented 4 years ago

@drc007 That could be an idea. When we first started this project we (DNDi) thoughtwe'd be able to send a set of close analogues, but turned out we no longer had access to them. If there is a way to put put out a crouwdsourcing request we should do so.

MFernflower commented 4 years ago

A common SHDI is commercially available from Sigma NL for screening use (But is a tad pricy) - https://www.sigmaaldrich.com/catalog/product/sial/45371?lang=en&region=NL

If I had to put lunch money on the target of the aminothiazoles - I'd say they are either enolase or succinate dehydrogenase inhibitors

kym834 commented 4 years ago

@drc007 @bendndi Agreed. If we can get our hands on some compounds through crowd sourcing we should absolutely do that. I'm happy to still synthesis a fresh sample of the MMV006357 and I can also look into the synthesis of any amionthiazoles that we would like for the SAR that we can't get our hands on either through a crowd source or by purchasing directly.

@bendndi Those compound suggestions look like a good starting point and align with what I was going to suggest, exploring the position of the nitrogen in the pyridine rings and some ring substitutions. I also think that some 4,5-substituted aminothiazoles would be worth looking at. From what I have read this will help with the microsome stability. And those that had lower rates of metabolism (<25% metabolised in 30 minutes) in both hamster and mouse microsome in the data you shared (#2) were all 4,5-substituted aminothiazoles. May not be overly important right now but I think it is still worth seeing what happens when the hydrogen is replaced in terms of activity.

MFernflower commented 4 years ago

@drc007 @bendndi @kym834

Here's what I thought up:

mandrakeaminothiazole

wwjvdsande commented 4 years ago

@drc007 @bendndi @kym834 We have tested a succinate dehydrogenase inhibitor in the past. I don't We did not publish this yet. It was siccanin. image For strain mm55 we had an IC50 of 0.092 ug/ml. The MIC was 4 ug/ml. MICs for 7 other strains ranged were also 4 or 8 ug/ml. The MIC50 was 4 ug/ml. The IC50 measured for M. mycetomatis was comparable to the IC50 of Trichophyton mentagrophytes (IC50 of 0.1 ug/ml) (Nose et al., J Bact, 1971, p 176-184).

Flutolanil is also tested. image It was part of the pandemic box. If did not inhibit M.mycetomatis growth at 25 uM and was therefore not tested further. Which compound do you prefer to have tested as well?

MFernflower commented 4 years ago

@bendndi @mattodd It is also important to note that 2-amino-4-(2-pyridyl)thiazole had human cell toxicity - so fibroblast tox assays are critical for this series!

kym834 commented 3 years ago

An update on synthesis

I've mapped out a route to the hit compound (see below). We should be able to access a very wide range of analogue using this route as well.

MMV006357 Synthesis Route

I'm still waiting on the 2-amino-4-methylpyridine to arrive but have successfully made the brominated intermediate required for the final step of the synthesis along with the 3-pyridinyl, 4-pyridinyl and phenyl analogues. For interest lab notes are here

While I'm waiting, we have 2-aminopyridine in the lab so I'm going to start with the to synthesis the following compounds

If this initial synthesis goes well we are planning to run some of this synthesis route with the SSP students at the University of Sydney later in the semester (April-May). I'll update a little on this in the meeting tomorrow and again once we have work out all the wrinkles.

PaulMcKeatingSevenoaks commented 3 years ago

Hi We’ve been looking at this at Sevenoaks School as a possible next place to look after some fenarimols. It’d be interesting to find out how it’s going for you and if we could contribute in the future.

kym834 commented 3 years ago

Hi All,

MMV0006357 has been synthesised and characterised and is ready to be shipped for testing (after it has been assigned a MYOS number (#5)).

Here is the synthesis route that I used

I've found it to be a robust synthesis route and we have used it to make another 12 analogues with first year students at The University of Sydney. I'm going to write up a summary of what we did in more detail in a new issue

@PaulMcKeatingSevenoaks This went quite well for us and I think there is a lot of room to build this series with high school and undergraduate students.

wwjvdsande commented 3 years ago

That's great. When ready please let us know.

PaulMcKeatingSevenoaks commented 3 years ago

This looks really promising, thanks, @kym834

(And a cool ring-forming reaction for school students!)

kym834 commented 3 years ago

@wwjvdsande Et al. have tested the re-synthesised MMV0006357 and we have confirmed it's activity!

Details have been added to the wiki so closing this issue.