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OpenSourceMycetoma / What-other-molecules-to-screen

Suggestions for New Series for MycetOS
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What other molecules to screen #1

Open wwjvdsande opened 5 years ago

wwjvdsande commented 5 years ago

We started the MycetOS project by screening the pathogen box and the stasis box. We now additionally screened the pandemic box. The results can be found here. As you can see, from the 400 compounds screened, 45 were active at 25um. there are interesting hits in here. Does anyone know if there are additional compound libraries available which will be interesting to look further into? The most interesting would be to find two additional chemical compound series with a different mode of action than CYP51 (the target of the azoles and the fenarimols) which we could explore.

wwjvdsande commented 5 years ago

Pandemic box for github.xlsx

Hereby the list of molecules.

wwjvdsande commented 5 years ago

@mattodd @bendndi Hereby additional molecules identified in the pandemic response box from MMV.

mattodd commented 5 years ago

Great, thanks for posting @wwjvdsande (and for starting this new repo). This issue is an excellent place to discuss the results of the Pandemic Response Box screen that was being discussed over at OpenSourceMycetoma/Series-1-Fenarimols#3 First things first, we need a diagram of the results with compound structures. @dmitrij176 can you please work on creating this? Initially just the 45 compounds that are active at 25 uM. Then we can consider synthetic feasibility, find analogous compounds and consider likely MoAs.

Quick Q: @wwjvdsande are the new data from the Pandemic Box added to the Master List already? If not, could they please be pasted in?

dmitrij176 commented 5 years ago

@mattodd already working on it

drc007 commented 5 years ago

@mattodd @wwjvdsande A rather left field idea. How about screening the Cysteine Covalent library from Diamond? https://www.diamond.ac.uk/Instruments/Mx/Fragment-Screening/Fragment-Libraries/Other-libraries.html

Contains a number "privileged" structures (benzyl piperidine, aminothiazoles) attached to warheads.

MFernflower commented 5 years ago

@drc007 Very interesting idea!!!! Are the payloads all the same (e.g epoxide) or do they vary?

drc007 commented 5 years ago

Mixture of unsaturated carbonyl and chloroketones.

I reviewed it here https://www.cambridgemedchemconsulting.com/resources/lead_identification/covalent.html

MFernflower commented 5 years ago

@drc007 Kinda calls back to my phenothiazine idea (Proposed series 3) from like a year ago - have a not so pretty drug that hits multiple targets at once and can be further optimized

MFernflower commented 5 years ago

@dmitrij176 Do open another github issue once you have finished it

MFernflower commented 5 years ago

@mattodd @drc007

I also made a call to screen the OSM-S4 malaria drugs against this fungus quite a while back

https://github.com/OpenSourceMycetoma/General-Start-Here/issues/8

bendndi commented 5 years ago

@wwjvdsande what would be the throughput of your assay - i.e. how long did it take to screen the boxes (400 cmpds each) and would you be able to deal with an increase in order of magnitude (4,000 cmpds, 40,000 cmpds?)

bendndi commented 5 years ago

I think the most interesting result on first glance is that Olorofim seems very active... So ticks the box of a non-CYP51 inhibitor. It's a DHODH inhibitor so hits the pyrimidine biosynthesis pathway. image

Key paper here

@wwjvdsande is this something that was already known as being active against mycetoma? Oerhaps we could contact the team behind Olorofim and see if they would share some of the library of compounds from the screen?

bendndi commented 5 years ago

The company behind Olorafim: https://www.f2g.com/

It's currently in Phase IIb for aspergillus. They have some interesting comments here on the compassionate use: https://www.f2g.com/compassionate

@wwjvdsande do you think we could rapidly prioritize further investigation of this compound? If we get some decent data in the next phase of studies (larvae?) we could approach them (we= MycetOS or DNDi or both)

wwjvdsande commented 5 years ago

@bendndi we tested olorofim already. We collaborated with f2g on this separately before we screened the pandemic box. The manuscript is currently under revision. We did screen in vitro only, not in the larvae. It has potent in vitro activity however the vehicles used to solubulize olorofim where toxic to the larvae so testing olorofim in larvae was not possible in the past. During the ECTMIH last week we had an oral on this compound and during TIMM next week we will have a poster.

wwjvdsande commented 5 years ago

MMV also mentioned that there is a large library available for DHODH inhibitors, developed against plasmodium and bacteria. They could help with that library.

wwjvdsande commented 5 years ago

@wwjvdsande what would be the throughput of your assay - i.e. how long did it take to screen the boxes (400 cmpds each) and would you be able to deal with an increase in order of magnitude (4,000 cmpds, 40,000 cmpds?)

If a technician can work on this constantly, it will speed things up. However, the problem is that I don't have the funds to do that. We screen these compounds now in the time left between the experiments needed for other projects. So when I have a dedicated technician, we could screen the first screening (100 uM) in triplicate within a month for 7500-10000 compounds easily. It might also mean we have to switch to another viability dye to keep it affordable. This means we will only have data on if the fungus is inhibited by 100 uM of a compound. No IC50 yet, but that will only be done by the compounds which are potent.

mattodd commented 5 years ago

The DHODH library is a great idea. Happy to pursue this with MMV with you, Wendy. Any similar resources available via DNDi contacts @bendndi?

On Thu., 3 Oct. 2019, 09:19 Wendy van de Sande, notifications@github.com<mailto:notifications@github.com> wrote:

@wwjvdsandehttps://github.com/wwjvdsande what would be the throughput of your assay - i.e. how long did it take to screen the boxes (400 cmpds each) and would you be able to deal with an increase in order of magnitude (4,000 cmpds, 40,000 cmpds?)

If a technician can work on this constantly, it will speed things up. However, the problem is that I don't have the funds to do that. We screen these compounds now in the time left between the experiments needed for other projects. So when I have a dedicated technician, we could screen the first screening (100 uM) in triplicate within a month for 7500-10000 compounds easily. It might also mean we have to switch to another viability dye to keep it affordable. This means we will only have data on if the fungus is inhibited by 100 uM of a compound. No IC50 yet, but that will only be done by the compounds which are potent.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHubhttps://github.com/OpenSourceMycetoma/What-other-molecules-to-screen/issues/1?email_source=notifications&email_token=ABBO2NJGRURNKLOHUIU7OPLQMWTKNA5CNFSM4I32LEDKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEAHM2BY#issuecomment-537840903, or mute the threadhttps://github.com/notifications/unsubscribe-auth/ABBO2NKS3K6HGHUYZANTQBLQMWTKNANCNFSM4I32LEDA.

bendndi commented 5 years ago

@wwjvdsande Any idea who would be the best person at MMV to approach regarding these DHODH compounds? Also, do f2g have a library of compounds from the med Chem efforts - is that what your manuscript is about?

Also would be good to understand what is and what isn’t possible for vehicles for larvae model - could we (mycetos) look into other alternative vehicles for olorofim, or is that not possible?

wwjvdsande commented 5 years ago

We only tested olorofim. It is their lead compound and as you mentioned available for passionate use. That's why we were interested to see if Madurella was inhibited by this compound. We compared in silico the target proteins and than later in vitro susceptibility tests agains a larger pannel of madurella mycetomatis isolates to determine if it was potent. F2G should have a larger library on these compounds as olorofim was selected as the best. For F2G it might not be that interesting to look into other vehicles as the vehicles used were effective in mouse models. They tested everything in mice. Unfortunately I can't do this is mice without funding. We have a mouse model but it is currently not up-and-running, if we want to use this model we need to invest in it and get clearance. That's why I could not do that yet.

MFernflower commented 5 years ago

Returning back to the cyp51 side it's interesting how good eberconazole is - should mean that the ring locks @fantasy121 are working on might show a decent potency

@wwjvdsande @mattodd @drc007

mattodd commented 5 years ago

(offline discussion happening with MMV/partners to access DHODH-related compounds, will report ASAP).

MFernflower commented 5 years ago

I'm always a little cautious about DHODH inhibiting compounds - they can be ferociously teratogenic!!!!

olorofim is said to be safe as it shows virtually no affinity to the human enzyme - but if we make analogues we would need to find someway to test them so we can avoid human enzyme cross binding

@wwjvdsande @mattodd @bendndi

Wilson-Lm commented 5 years ago

We have only screened olorofim in vitro. Not in the larvae. We were told by F2G (the company that provided olorofim) that the vehicles used to solubilize olorofim where toxic to the larvae, so testing olorofim in larvae wasn't possible.

Wilson

wwjvdsande commented 5 years ago

We are currently in contact with Jeremy Burrows from MMV. He knows a collection of DHODH inhibitors which has been developed to be more specifically towards pathogens and which is hardly active against the human enzyme. Might be worth screening that collection.

bendndi commented 5 years ago

Thanks for the info everyone. I have a couple of questions:

-@wwjvdsande @Wilson-Lm When dosing to larvae what vehicles do you usually use, and is it essential that the test articles are fulliy in solution in the vehicle, or can a homogenous suspension be tolerated?

wwjvdsande commented 5 years ago

@bendndi @mattodd I know some people at F2G and will ask these questions. Furthermore Saskia du Pré is currently doing a post-doc in our lab, she has worked with this compound during her PhD so she knows a lot of it. She will return on monday so I will ask her to join us here as well. Upcoming week TIMM (trends in medical mycology) will be in Nice. I will go there and they will be there too, so I can talk to the people from F2G in person as well. That is usually better. We will have a poster on our olorofim data there, so for anyone interested please stop by.

@ bendndi For the larvae we usually use a 5% DMSO in PBS solution, they tolerate that but we cannot go higher on the DMSO because that becomes toxic. For amphotericin B and terbinafin we also used a 5% glucose solution which they also tolerate very well, there we had issues with the solubility too and this worked best. I don't know if it will be a big deal for the larvae if the paricles are not completely in solution, we did not have that issue yet. However it needs to be bio-available. So the larvae needs to be able to process them if they are not. With rats in an aspergillosis model we had issues with a compound in the past which had solubility problems. It was actually piling up in the tissues, you could find them there in large quantities and we were not sure how much was actually in serum. Of course we can determine the concentration in hemolymph by plate assays. We had done this in the past with itraconazole, voriconazole, amphotericin B etc. but at the moment I don't know how the larvae will respond on the particles. We can only test and find out I guess when we need to.

wwjvdsande commented 5 years ago

So I'm more than happy to test this, but it will take some time. The larvae season ends around november and starts up again in march. During the winter the larvae often don't survive it when we transfer them to 37 degrees.

wwjvdsande commented 5 years ago

We can than only do assays at room temperature and that does not go well with the fungus. Toxicity could be done and formulations could be done, but I will have to check later if room temperature results are the same as 37 degrees.

MFernflower commented 5 years ago

@wwjvdsande Would it be possible to do a tox screen in Drosophila until the larvae are ready?

Thoughts @bendndi ??

wwjvdsande commented 5 years ago

@MFernflower I'm not sure if that will help. Drosophila is of course a different organism that Galleria mellonella. I think tox screen in Galleria mellonella at room temperature would then be more feasible. It will have a higher chance of being comparable to tox screens at 37 degrees. A compound toxic at room temperature will most likely also be toxic at 37 degrees.