[Long term open issue] Testing series four's ability to kill things other than malaria

[MFernflower]

I have mentioned this a few times before but I believe it would be best to leave this as a long term standing issue: Can the S4 drugs kill other pathogens besides Plasmodium falciparum? (Also, do these drugs work on vivax?)

I would be really interested in seeing if these drugs could kill TB (Wellcome trust will do this pro bono) and perhaps pathogenic free-living amoebæ like Nægleria Fowleri (Easily grown on coli plates) and Balamuthia mandrillaris (requires a special lab)

I understand this is low on the priority list but I would love to hear peoples opinion on testing against these organisms!

[holeung]

That would be an interesting experiment. If S4 work by targeting ATPase4, then they are more likely to be effective in organisms closely related to plasmodium, with high sequence conservation of ATPase4. A quick search shows toxoplasma and cryptosporidium as the common pathogens with the most closely related ATPase4. TB, as mycobacteria, is not closely related.

[MFernflower]

Could you do a quick check to see about Nægleria Fowleri? @holeung

I know some fungi and fungal-like protists have some pumps on their membrane that could be inhibited by these drugs

[MFernflower]

I assume that COADD would be able to do the bacteriological testing pro bono?

The issue is going to be getting a lab to test a few of these drugs against Toxoplasma gondii and Nægleria fowleri respectively

Another interesting target would be Cryptococcus neoformans as it is a Basidiomycete (being closely related to certain mushrooms) and there are several fungicides that work via pump inhibition... We may have drug class on our hands that could cure multiple different ntd's !!!!

@holeung @mattodd

[mattodd]

Thanks for raising this @MFernflower . The short answer is YES, we ought to be testing these compounds against other pathogens, all the time, by default. This was one of the rationales for ensuring we had good stocks of the Frontrunner set (#400). The bigger picture is that we'd like to have a mini "OSM-Box" of compounds that people could request, unencumbered by IP constraints, inspired by MMV's work in this area.

So what's the constraint? As usual, it's Time.

If people can identify assays to which we can submit compounds, and which involve a) a decent scientific rationale (since we are always resource-limited) and b) principles of open data , then we can ship things. What people need to do is contact the people who run those assays and see whether some OSM compounds can be accepted. And how they should be delivered, and how many compounds can be examined, etc. Building relationships like this takes a little time, to make sure everything is clear.

In fact we've already done a little bit of this. The data aren't public yet purely because of other things in OSM taking precedence, and I was wondering about the best way to make the data public since we have been evaluating a few compounds against pathogens that are beyond malaria, so where do the data go? Any thoughts on this, everyone? I'd been wondering about writing up a step-by-step on how to perform a single screen of known compounds and publish it as a mini-paper/preprint/dataset from where the data could most easily feed into pubchem. @cdsouthan

The data I have sitting on my hard drive waiting to go public are screens of several compounds (including some OSM's) against H. Contortus in the lab of Robin Gasser in Melbourne (assay) (gave no hits, sadly) and a CO-ADD screen that identified OSM-S-293 as a confirmed hit vs C. Albicans (inactive against other things). I need to share the data properly, so we can perhaps a) think how best to exploit the hit, and b) think what to target next. This would need considerable community input clearly, since the team here in Sydney are quite swamped just with the malaria work and only have limited bandwidth at the moment for stepping beyond that - as you can see from the delay in sharing the very nice Albicans hit... Comments and advice welcome, particularly re

a) best methods for datasharing these individual non-malaria assays b) high-value screens and how to get them done c) mechanisms (beyond my lab) of ensuring we have stocks of good OSM compounds. Chris S - we've spoken before about this. Perhaps one for company philanthropy or schools-based crowdsourcing @alintheopen where compounds could be maintained at e.g. Compounds Australia, ready for shipping.

[MFernflower]

"and a CO-ADD screen that identified OSM-S-293 as a confirmed hit vs C. Albicans (inactive against other things" I'm currently learning mycology and this is an interesting thing to be because if it's effective against an ascomycete I would be curious to see if it works against a basidiomycete (Cryptococcus neoformans) and a fungus-like pathogen (Nægleria fowleri). This is is a long term goal and will not be completed in the near future but I think this is important planning that needs to be done @mattodd

I might be able to talk with the leader of the mycology club as he has some contacts but there is no guarantee

[holeung]

Shared sequence identity with Naegleria gluberi (Fowleri genomic data does not seem to be available yet) is 32%. For Candida albicans, it's 30%. ~30% is pretty low so I am surprised about the hit vs. C. albicans. For Haemonchus contortus, it's also 30%. Attached is the sequence homology analysis with BLAST against eukaryotes.

NCBI Blast_Protein Sequence.pdf

[MFernflower]

35% for Cryptococcus!

If I had to pick two organisms to test OSM-S-293 against I would vouch for Cryptococcus neoformans and Nægleria fowleri

@mattodd @holeung

[holeung]

Sequence identity with toxoplasma is 55%, and cryptosporidium is 45%. I don't think there is strong interest in targeting these organisms as they generally are associated with mild disease except in immunocompromised patients. There is strong interest in developing antifungals vs C. albicans and other pathogenic fungi. My knowledge is limited to human diseases. It would be good to have someone look over the list to see what pathogens are important for animal disease.

[mattodd]

Ok, please let me jump in here. If people are interested in particular screens can people please please to provide a little rationale (e.g. a lit reference to any existing screens vs that organism, or some clear indication that screens for new compounds are urgently needed) AND a location of a person who is known to be running the assay right now. The people who contributed to the construction of the Pathogen Box might be a good starting point?

[drc007]

I presume other OSM compounds were tested in the CO-ADD screen? If so and they are inactive I'd have thought it unlikely that they are acting via the same molecular mechanism ATPase4? For data sharing the simplest method would be to create another Google doc spreadsheet with a column for each assay.

[cdsouthan]

I beg to differ. I would take up @mattodd s point on limited bandwidth and suggest "we" (i.e. the OSM enterprise) stay focussed on malaria, AWAK there is still loads more to be done to get anywhere near a clinical candidate and its not certain that Series 4 will deliver such. NOBA there still seems to be a chronic shortage of reciprocal lead x-screening and/or mechanistic deconvolution even between the major malarial strains. I'm also not completely sanguine about the box approach since none of my 22 antimalarial lead recomendations made it in https://cdsouthan.blogspot.se/2014/06/getting-into-box-with-some-recent.html (possibly related to patent issues). Also, beyond the boxes that MMV managed to their credit, there seems no community solution to the cross-supply of leads beyond the level of collegial swapping that has always taken place. I tried smoozing with suppliers again at Pharmacology 2016, even suggesting they could sell Series 4 front-runners just at cost but got nowhere. OSM should ensure that, along with basic assay results in PubChem BioAssay, robust synthetic protocols are in the open, so anyone can pick them up, including groups working on other pathogens and who are experts in their own specialised assays (and a basic set of their results should also find their way into PubChem). Obviously @alintheopen 's pioneering idea of "pharming" out lead re-synthesis to schools and universities (to stock Compounds Australia?) should be pursued

JFTR I'm not convinced that pathogen lead x-screening based on "average" orthology is supported by whole cell assay data. AWK for validated in vitro targets this could be rationally based on sequence identity scores and even more so if structures are available.

[mattodd]

Sure @drc007 the sharing of the data as a Google sheet is trivial (thanks to conversations we've all had on this subject) and can be accompanied by descriptions of assay methods from those people performing them. But where do these go, for maximal effect?

We can post them to an OSM lab book. We could post a report to Figshare, or Sydney Uni's repository. We could try to draft a Minimally Publishable Unit for a journal. What's best, in terms of piping the data into the most widely-employed databases, so that the results will be found most easily? What's the best method here that scales, so that others (interested in those other pathogens) can do the same kind of thing autonomously?

A new journal, The Cross-Screening Digest, anyone?

[cdsouthan]

"most widely-employed databases, so that the results will be found most easily?" = PubChem BioAssay, its that simple :) See https://www.ncbi.nlm.nih.gov/pubmed/27899599 "PubChem BioAssay: 2017 update"

(n.b. possible conflict of interest declaration: folk from PubChem have brought me beers at ACS and BioIT)

Drafting a manuscript (by template even) that will eventually be picked up by ChEMBL is also excellent with full M&M descriptions and for J.Med.Chem. you can add a SMILES activity sheet as supp dat (but SciFinder will pull it out anyway). This will duplicate into PubChem BioAssay (with identical structures on a good day) but currently takes ~12 months (excluding the writing time). Note BindingDB replicates ChEMBL entries that have assigned protein targets, and offers complementary ways of analysis/filtration. Beyond these three coupled databases for SAR collation and easy download, all other open repositories are more or less data toombs at the present time (but this is not a criticism of their efforts)

Note also option 2 gets a fully attributed publication that boosts the careers of all authors (e.g. that Mat < full Professor soonest)

[mattodd]

Excellent, @cdsouthan thanks, that's great. With all the meta info there (i.e. authorship, brief backstory) I think this may be what we're looking for. Example here. It's selfishly useful for academics to be able to cite such things as evidence of work, and such a page is sufficiently permanent and citable to count, while also providing ease of discovery.

Do people agree? Anyone have any experience at a manual submission of this type?

[drc007]

@mattodd @cdsouthan I've sent an email to Ruth Neale at CO-ADD to see what they have done, no point in re-inventing the wheel.

[MFernflower]

@drc007 Great idea... Would it also be possible to ask if they (COADD) do screening against Cryptococcus neoformans and Nægleria fowleri?

[drc007]

@MFernflower I don't think so. Full details here. http://www.co-add.org/content/free-screening

[MFernflower]

@drc007 @mattodd Cryptococcus neoformans is done for free at COADD!!! Could we send a few compounds there way sometime? As for Nægleria fowleri.. We are stuffed unless somebody wants to do the testing for free... I think there is a charity just for Nægleria here in the USA (http://www.kylelewisamoebaawareness.org/) so they might be able to help??

[cdsouthan]

Not really OSDD? Adding the ChEMBL release cycle (and patents to publish?) we're talking ~3 years surfacing time. Note also nothing from this outfit has come through into ChEMBL 22 ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_22_1/chembl_22_1_release_notes.txt

[MFernflower]

That's pretty poor @cdsouthan

Im wondering if I should close this issue beause we cant find a testing lab to do these screens? @mattodd

On Feb 7, 2017 2:47 PM, "cdsouthan" notifications@github.com wrote:

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[drc007]

@MFernflower This issue has only been open 5 days! I'd leave for a little longer to allow time for infrequent visitors to comment.

[cdsouthan]

Agreed, these open discussions are useful so no rush to "close" As a summary so far perhaps 1) active engagement with cross-screening outside malaria would not currently be considered a priority for OSM resources 2) we obviously welcome utilisation of our results (including synthetic protocols) by others outside malaria 3) some issues touched on above are perennial and can be extended under other to-dos (e.g. intra-malarial compound sharing and data surfacing in PubChem)

[mattodd]

Let me summarise where I think we'd be most effective.

1) OSM's day-to-day is malaria. 2) A core feature of the project is the open source aspect, which must involve full protocols for everything, via the lab notebooks. This enables anyone to make all the molecules for themselves. 3) Nevertheless, it can be advantageous/barrier-lowering for there to be a central stock of the most promising antimalarials. We've tried to take this approach with the Frontrunners. In large part this makes internal OSM sense since we often come to realise that further evaluation of promising compounds is necessary. We can't centrally maintain stocks of everything, but an OSM-Box is relatively low effort if it additionally encourages: 4) ... members of the scientific community identifying gaps where OSM-Box compounds have not been evaluated for some activity/property. In such a case we could make it clear that members of the community are encouraged to identify possible applications of the compounds and request that samples be sent for evaluation somewhere.

If we maintained an OSM-Box at Compounds Australia, the shipping out would be relatively simple and cost effective.

If this seems reasonable (please chip in), we could include some How-To text on the wiki somewhere detailing all of this.

We could then publish a short note somewhere describing this approach and advocating that other labs maintain similar Boxes of the most promising compounds, and advocating for the publishing of the outputs into Pubchem along the lines of the discussion above.

[cdsouthan]

An OSM-Box sounds great. Extending it beyond the front-runners with a few low-activity controls would be good, as well as including other selected non-OSM leads (which the MMV boxes didn't really cover). I could assist with ensuring these were all mapped into PubChem

[MFernflower]

Will a box of the anti-fungal hits be stocked as well? Mycobox has a nice ring to it! @cdsouthan @mattodd

[JZuegg]

CO-ADD screened the compounds against Cryptococcus neoformans (H99; ATCC 208821) , so if we confirmed only activity against C.albicans, the activity against C.neoformans must have been below the threshold in the primary screen (80% inhibition @ 32 ug/mL). However, CO-ADD won't venture into parasite screen any time soon, so we can't help you there. We would like to screen molds though, but haven't managed to get the assay against Aspergillus fumigatus up and running... Let us know if confirmation (MIC) against C.neoformans is useful for your publication efforts.

For publication of data, CO-ADD can submit data directly to ChEMBL (strategic partner of CO-ADD) to be included in their next release. The option there are either with a publication as a reference, by issuing a DOI as a reference, or under the CO-ADD banner (not defined yet). So let me know, as we are happy to prep the data for ChEMBL import and sort out the issuing of a DOI (either by ChEMBL or here at UQ). The DOI would point to your set of data at ChEMBL.

An additional option I mentioned to an email to Chris is CDD (https://www.collaborativedrug.com/) where you can setup your own OSM collaborative site. I ran into the CEO of CDD a few days ago, and he's very keen to get more open/public projects into CDD (like they have done with TB Alliance)... Let me know I can get you hooked up.

And yes, let us know when you have a OSM-box or mycobox ready as we are happy to run them through our screen, especially if you have them at CpOz, which we use as storage and for plating as well. (j.zuegg@uq.edu.au; info@co-add.org)

[MFernflower]

@JZuegg Random question.. I'm wondering if you could figure out a screen against the fungus-like flagellate human pathogen known as Nægleria fowleri - They grow really well on EColi lawn plates kept at 38 or 39 °C

[JZuegg]

In principle. Quick search found Naegleria fowleri from ATCC and a few published protocols to test it in a broth system. The devil lays usual in the details, especially scaling it to 96 or 384 plates. Any development and validation would take considerable time. I'll check with our microbiologist.

[cdsouthan]

@JZuegg Thanks and JFTR I'm on the SAB of CDD and so am aware of the powerful cross-platform integration and standardisation it offers. Coincidentally I also just viewed a slideshare set where Pollastri extols its virtues. Nonetheless, the closed consortium model (however large that consortium) is still not entirely concordant with the OSM Gospel according to @mattodd and his disciples (implicitly including ourselves of course :) https://www.ncbi.nlm.nih.gov/pubmed/23985301

[drc007]

http://www.cambridgemedchemconsulting.com/news/index_files/292de120ff03dbaddd9a14cb9224df39-262.html WHO publishes list of bacteria for which new antibiotics are urgently needed

[MFernflower]

@drc007 Mr.Swain, Do you know if there is a list of fungi too? I do not think these drugs will kill bacteria as the proposed transporter they hit is only found on eukaryotes

[Jake-s16]

Don't some other antimalarials also kill Babesia species? Maybe another group to look at.

[MFernflower]

@Jake-s16 Toxoplasma as well.. But the real ticket is showing that these drugs are fungicides

[drc007]

I suspect that any activity against fungi will be via a different mechanism

[MFernflower]

@drc007 Fungi have very similar ATPases on their membranes - see @holeung 's comparison https://github.com/OpenSourceMalaria/OSM_To_Do_List/files/756230/NCBI.Blast_Protein.Sequence.pdf

[MFernflower]

In a perfect world we would be able to throw 4 of our most potent TP's at Nægleria, Cryptococcus and Blasto.... Sitback and watch the carnage but time is a huge limitation!

[MFernflower]

@mattodd Would you consider sending two active S4 and two inactive S4 drugs to COADD for testing against C. neoformans provided they can return the results within two months of them receiving the compounds?

[JZuegg]

Dear Todd,

Just to let you know, we are closing CO-ADD screening in the second half of December, for maintenance of assay/strains and calibration of equipment, as well as holiday over the Xmas period. We’ll restart screening in the second week of Jan-2018.

For any ‘fast’ results we would require the compounds with us in the next weeks. Happy to run small batches as MIC right away.

Cheers Johannes

Dr. Johannes Zuegg Community for Open Antimicrobial Drug Discovery Institute for Molecular Bioscience | The University of Queensland | Brisbane 4072 | Australia T +61 (0)7 3346 2994 | E j.zuegg@uq.edu.aumailto:j.zuegg@uq.edu.au | Skype j.zuegg.uq | W www.co-add.orghttp://www.co-add.org/

[Co-Add_Logo_Web_Baseline]http://www.co-add.org/

From: Anthony S. [mailto:notifications@github.com] Sent: Wednesday, 8 November, 2017 13:46 To: OpenSourceMalaria/OSM_To_Do_List OSM_To_Do_List@noreply.github.com Cc: Johannes Zuegg j.zuegg@imb.uq.edu.au; Mention mention@noreply.github.com Subject: Re: [OpenSourceMalaria/OSM_To_Do_List] [Long term open issue] Testing series four's ability to kill things other than malaria (#482)

@mattoddhttps://github.com/mattodd Would you consider sending two active S4 and two inactive S4 drugs to COADD for testing against C. neoformans provided they can return the results within two months of them receiving the compounds?

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[MFernflower]

@david1597 Do you have two active s4's and two inactive s4's to send off to @JZuegg within the next week or so? Paging Dr.Todd!