Difference between revisions of "OpenSourceMalaria:Story so far"

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The compounds evaluated to date (assigned OSM codes) can be viewed: [http://malaria.ourexperiment.org/osm_procedures/group/Compound%20List picture list], [https://github.com/OpenSourceMalaria/OSM_compounds .sdf], [http://bit.ly/OSDDcompounds old spreadsheet]. The first 100 compounds were [https://www.ebi.ac.uk/chembl/malaria/doc/inspect/CHEMBL2113921 uploaded to ChEMBL].
The compounds evaluated to date (assigned OSM codes) can be viewed: [http://malaria.ourexperiment.org/osm_procedures/group/Compound%20List picture list], [https://github.com/OpenSourceMalaria/OSM_compounds .sdf], [http://bit.ly/OSDDcompounds old spreadsheet]. The first 100 compounds were [https://www.ebi.ac.uk/chembl/malaria/doc/inspect/CHEMBL2113921 uploaded to ChEMBL].
===Series 1 - The Arylpyrroles===
[https://plus.google.com/u/0/b/114702323662314783325/115627447826173336765/posts Paul Ylioja] started Series 1 by resynthesising the two known active compounds from the GSK set (OSM-S-5 and OSM-S-6 - structures below), plus a few simple derivatives, and [http://www.thesynapticleap.org/node/367 confirming that they were active]. The [http://malaria.ourexperiment.org/biological_data/month/1325376000 biological evaluation] was carried out by three separate labs ([http://www.discoverybiology.org/team/vicky-avery Vicky Avery], [http://www.bio21.org/group-leaders/bio-chemistry/stuart-ralph Stuart Ralph] and the [http://www.gsk.com/collaborations/tres-cantos.htm original GSK Tres Cantos Lab led by Javier Gamo]) to ensure a solid footing of repeatability. The original compounds contained an ester which was thought likely to hydrolyze ''in vivo'', so various versions of the "lower half" of these leads were also evaluated to check whether the original hits were prodrugs, but all these compounds were found to be inactive. The project champion from MMV, [http://www.mmv.org/about-us/our-team/paul-willis Paul Willis], [http://www.thesynapticleap.org/node/349 recommended] a few "near neighbor" compounds that also looked interesting, and a number of these were made too and evaluated in this first round. One compound, OSM-S-9, was found to be more active than the original GSK hits. [https://plus.google.com/u/0/111817031902595048944/posts Sanjay Batra] came on board the project and his student [https://plus.google.com/u/0/113151089809892205923/posts Soumya] made (and is making) [http://malaria.ourexperiment.org/cdriarylpyrroles some analogs] varying in the position of the fluorine atom, though the activity of those tested to date is low. (Sanjay works at the [http://www.cdriindia.org/analytical.htm CDRI] in Lucknow, India, where [https://plus.google.com/u/0/116616719379353298385/posts Saman Habib] also works - Saman is leading the [http://malaria.osdd.net/ Indian OSDDm project] which will hopefully get started soon). The outcome was that the original hits remained interesting (because of their reasonable potency and logP values) but that highly potent novel antimalarials were also being generated in this class. Thus a [http://www.thesynapticleap.org/node/381 second set of compounds was synthesized and evaluated], giving rise to several new highly potent compounds, one of which (OSM-S-39) displayed a picomolar IC50 value. This is impressive given the small number of compounds made to date, and is testament to the quality of the hits contained in the original GSK set.
[[Image:Compounds of Interest in Update.png|thumb|center|500px| '''Original and Representative Potent Compounds in the Arylpyrrole Series]]
It was decided to move the most promising compounds on to advanced biological evaluation, to assess the promise of this class early rather than continue to increase potency through analog synthesis:
* '''Metabolic and solubility assays''': The two original GSK compounds (OSM-S-5 and OSM-S-6) and six other compounds made in this project were evaluated by [http://www.pharm.monash.edu.au/staff/sacharman.html Sue Charman's lab at Monash] for their stability in phosphate buffer. The raw data are [http://malaria.ourexperiment.org/biological_data/3101 here] and can be discussed [http://www.thesynapticleap.org/node/401 here]. The GSK originals displayed good solubility but moderate degradation rates. The other compounds were degraded more slowly but at a cost of low solubility. Subsequently the original GSK compound OSM-S-5 was evaluated for stability in human and mouse plasma. The compound was stable in human plasma but susceptible to hydrolysis in mouse plasma. Esterase activity is known to be higher in rodents than in other species which was confirmed using a control compound in this assay (p-nitrophenol acetate) so the results are not too surprising. Lab book page [http://malaria.ourexperiment.org/biological_data/3598/Human_and_Mouse_Plasma_Stability_of_OSMS5PMY_106.html here]. A [http://malaria.ourexperiment.org/biological_data/6729/Glutathione_Trapping_Study_for_OSMS35_.html glutathione trapping experiment] was carried out on OSM-S-35 as representative of the Near Neighbour series, giving some identification of possible trapped metabolites, but the levels observed were not large.
* '''hERG''': One of the original GSK compounds (OSM-S-5) plus one of the most potent novel compounds identified to date (OSM-S-35) were subjected to the [http://malaria.ourexperiment.org/biological_data/2999 hERG assay and passed], perhaps implying that this class of compounds should not exhibit undesirable cardiac side effects. Discussion page [http://www.thesynapticleap.org/node/402 here].
* '''Late Stage Gametocyte Assay''': Four of the compounds have also been [http://malaria.ourexperiment.org/biological_data/3066 evaluated in a late stage gametocyte assay] with very interesting results indicating unusually high activity in blocking the transmission of the parasite. The original GSK compound OSM-S-5 was inactive. Discussion page [http://www.thesynapticleap.org/node/403 here].
* '''In vivo''': However, the two original GSK compounds as well as one of the most promising near neighbor compounds (OSM-S-35) were evaluated in mice and found to possess zero oral efficacy (Results available [http://malaria.ourexperiment.org/uri/ed here]). Subsequent analysis of the plasma samples from the trial with one of the GSK compounds (OSM-S-5) showed that the compound was indeed orally available, but levels in the blood were not being maintained. Raw data [http://malaria.ourexperiment.org/biological_data/3825 here]. 
Other discussions of the biological results described above can be found [http://www.thesynapticleap.org/node/405 here]. The choice became whether to change the focus of the OSM project to another compound series or whether to continue to alter the structures of the most promising compounds to overcome the ''in vivo'' roadblock described above.
A decision was taken to carry out a third round of analog synthesis and evaluation on the arylpyrrole series, with an emphasis on analogs a) with low logP and b) that lack the thiazolidinone heterocycle. It was decided for the moment to park the near neighbour thiazolidinones because despite potency and activity in the late stage gametocyte assay, the series [http://www.thesynapticleap.org/node/384 suffered from low solubility]. Should this set of compounds be re-started, an [http://www.thesynapticleap.org/node/400 automatic prediction of isosteric replacements] has already been done ([http://malaria.ourexperiment.org/in_silico_prediction/2954 data]).
A consultation was [http://www.thesynapticleap.org/node/409 started] and [http://www.thesynapticleap.org/node/412 occurred] asking for suggestions for the ten most appropriate compounds to make, and the ten most interesting for commercial procurement. Assistance came from [http://www.thesynapticleap.org/node/399 automatic searching of databases of commercial compounds coupled with similarity searching] based on the hit compounds or other sources. The final stage of the consultation took place [http://www.youtube.com/watch?v=ooM8kuo14Bg live online]. The lists of compounds were [http://www.thesynapticleap.org/node/416 finalised] and [http://www.thesynapticleap.org/comment/863#comment-863 confirmation was secured from GSK] that none of the proposed structures had been included in the original GSK screen; commercial compounds were ordered and synthesis commenced. In early November 2012, the team received results from the [http://www.thesynapticleap.org/node/430 biological evaluation] of the commercial compounds (having codes OSM-S-81 through 91) and the first synthetic compounds that had been completed. This set of compounds were found to possess low to negligible levels of activity. Though surprising, the date provided some interesting insights. For example, a forked series, the [http://openwetware.org/wiki/OSDDMalaria:Arylpyrazole_Series pyrazoles], looked attractive but so far all examples tested (e.g., OSM-S-92) were found to be inactive ([https://plus.google.com/u/0/b/114702323662314783325/114702323662314783325/posts/6JWcy32oAfx pictorial comparison]). It was clear that alteration of the portion of the molecule attached to the pyrrole tended to eliminate activity ([https://plus.google.com/u/0/b/114702323662314783325/114702323662314783325/posts/FwVznMNSRRB picture of this] and [https://plus.google.com/u/0/b/114702323662314783325/114702323662314783325/posts/MXnCqf4g9zx summary of the shortened analogs]). While not completely forbidden, replacement of the ester with amine or amide functionality was generally deleterious ([https://plus.google.com/u/0/b/114702323662314783325/114702323662314783325/posts/ei5duHLWnAL picture of this] and [https://plus.google.com/u/0/b/114702323662314783325/114702323662314783325/posts/5NfUwhvdRud direct amide/ester comparison]). Methylation of the terminal amide, or of the amine/amide replacing the ester, or adjacent to the ester also greatly reduces activity ([https://plus.google.com/u/0/b/114702323662314783325/114702323662314783325/posts/XhfXZJagjyz picture of this]).
The next batch of third round compounds were synthesised and evaluated in December 2012. As with the first batch, all of the compounds were essentially inactive (OSM-S-103 showed mild activity).
[[Image:tssfar.png|thumb|center|700px| '''Representative Compounds from the Third Round]]
At the end of 2012 it appeared that the series was producing diminishing returns but there remained a [http://www.thesynapticleap.org/node/429 small number of compounds] which needed to be made to complete the campaign - specifically isosters of the troublesome ester in the original GSK hit. Patrick Thompson, a collaborator from the University of Edinburgh built on Matin Dean's work on the [http://malaria.ourexperiment.org/tcmdc_ap/month/1356998400 sulfonamide] whilst Murray Robertson and Alice Williamson focused on synthesising further analogues of the [http://malaria.ourexperiment.org/near_neighbours near-neighbours], trying to find potent molecules with increased solubility. The near-neighbours were [https://plus.google.com/u/0/b/114702323662314783325/114702323662314783325/posts/W5Sdz8J3iur evaluated] and a number of potent compounds were discovered, some with lower LogP than the first set of near-neighbour compounds.
The OSM project has to date [http://www.thesynapticleap.org/node/414 had no luck] in securing donations of compounds from commercial suppliers. On considering some structurally 'similar' active compounds from the TCAMS set, the team have also decided to synthesise a few [https://plus.google.com/b/114702323662314783325/114702323662314783325/posts/LzxZxukacpn extra compounds] plus hybrids, in order to assess their biological activity.
'''What are the Compounds in Series 1 Doing?'''
What might this series of compounds be doing to the parasite to kill it so effectively? It's not clear. The original screens were whole-cell assays, so while it is known that the compounds are effective, it's not known what they are doing in any detail. Iain Wallace from ChEMBL has performed [http://www.thesynapticleap.org/node/387 a prediction] of the biological role of these compounds (as well as predictions for the whole "[http://www.mmv.org/malariabox Malaria Box]", which is a set of compounds MMV are providing to people for antimalarial screening, and for [http://www.thesynapticleap.org/node/398 all the antimalarials in ChEMBL]. Iain clustered the compounds as similarity maps, allowing visualization of the correlation between structure and predicted activity. Discussed also [https://plus.google.com/u/0/b/114702323662314783325/114702323662314783325/posts/F5B9nA2sJLr here]. One of the predictions was that the compounds in Series 1 should hit an enzyme known as DHODH, and GSK are at the time of writing screening some of the project's compounds against this enzyme (done - data need to be added). These predictions are made using informatics - a comparison of the structures of our compounds with other known compounds that have known activities. The argument is based on extrapolation. To evaluate whether the prediction is correct, a subset of compounds has been sent to [http://chemogenomics.med.utoronto.ca/hiplab/index.php Corey Nislow] at the University of Toronto for screening in a yeast-based assay that does not identify for sure what the compounds are doing (which is very difficult) but provides harder biological evidence for a role. There are [http://www.thesynapticleap.org/node/360 occasional other clues] about activity arising from studies of these, or related compounds, in the literature; in such cases it is not clear whether the activity is relevant to their antimalarial potency, or whether the compounds are highlighted in assays because they are frequently members of commercial libraries.
'''Remaining Possible Lines of Enquiry'''
Though the series has been parked, anyone is free to re-investigate. Of interest might be:
* Synthesise [https://plus.google.com/u/0/b/114702323662314783325/114702323662314783325/posts/X4yLmTsYPjv these compounds] that might arise from the cyclisation of the arylpyrrole side chain
* Evaluation of the [https://plus.google.com/u/0/b/114702323662314783325/114702323662314783325/posts/TxnSLznSMTV "other half"] of the original GSK hit containing the antipyrene
* A new search of the TCAMS data set [https://plus.google.com/u/0/b/114702323662314783325/114702323662314783325/posts/LzxZxukacpn revealed] other compounds similar to the original hits that could be used for generating "hybrid" compounds that might represent new targets for the series
===Series 2 - Triazoloureas===
===Series 3 - Aminothienopyrimidines===
Old text that needs adapting then deleting
Two other interesting-looking starting points from the GSK set, based on a [http://openwetware.org/wiki/OSDDMalaria:GSK_Triazolourea_Singleton triazolourea] and a [http://openwetware.org/wiki/OSDDMalaria:GSK_Amino-thienopyrimidine_Series thienopyrimidine], were the focus of [http://openwetware.org/wiki/User:Jim_Cronshaw James Cronshaw's] honours [http://figshare.com/articles/ThesisforUpload.pdf/102049 thesis] at Sydney University. The triazolourea (OSM-S-56) was found to be [https://plus.google.com/b/114702323662314783325/114702323662314783325/posts/QfynoBafbXt even more active] than the original GSK hit (TCMDS 134395). James has synthesised the [http://malaria.ourexperiment.org/aminotpseries/5827/Suzuki_coupling_using_the_same_conditions_that_are_used_to_generate_boronate_esters.html thienopyrimidine] series lead, and we are awaiting confirmation of the compounds antimalarial activity. If the lead compound is confirmed as active then it will be necessary to decide which, if either, of the series are to be taken on further. In general a strategy for the project is to decide as early as possible which series are looking attractive biologically, because there are still a lot of leads to pursue. If any of these structures look synthetically attractive to you based on your previous experience, please consider joining the project. Some of these molecules are quite straightforward to make and would be suitable for undergraduate lab classes.
/end of old text
==General Strategies==
==General Strategies==

Revision as of 15:51, 20 January 2014

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This is a human-readable summary of the open source malaria project to date. A less readable collection of all the relevant data from the various compound series can be found here.

The story so far in the open source malaria project

The OSM project is primarily concerned with taking public domain compounds that have shown good activity in killing the malaria parasite in cells and improving the properties of those molecules in order to discover a compound that can enter Phase I clinical trials. This is phenotypic drug discovery project focussed on the hit-to-lead phase.


In 2011 the Todd lab at The University of Sydney received funding for a pilot project in open source drug discovery from the Medicines for Malaria Venture (MMV). The project champion at the outset was Tim Wells. Jeremy Burrows came on board and led the suggestion to go after a few of the actives that had been placed in the public domain in 2010 by GlaxoSmithKline and others. Work got underway in the lab in August 2011. The team were successful in securing further funding from an Australian Research Council Linkage grant that has generated funding from May 2012 for three years.

OSM Project Structure

The scientific idea behind the project is familiar medicinal chemistry methodology - the aim is to find a small molecule that is effective for the treatment of malaria, and that involves generating new molecules and evaluating them. Based on the biological results new analogs might be made or the series might be abandoned and another selected. Decisions to abandon series may be taken early because there are plenty of other series that are very attractive from a medchem perspective.

The crucial difference with this project though (as described in the 6 Laws) is that everything is open, meaning all the experiments go on the web (including the ones that did not turn out well). All the data are available. Anyone can do anything they wish with the compounds, with the proviso the project is cited (see CC-BY licence conditions below). Anyone can take part - people may make molecules, offer guidance and input in other ways that change the direction of the project as it is happening, i.e. rather than the release of all data at the end of the project, data are released as the project is happening so that people can become genuinely involved in the research. Thus the iterative cycle of analog synthesis in response to biological data that is normally guided by luck and medchem intuition is now guided by the intuition of the collective. Similarly, since the biological data are all open too, it should be easier to form an objective assessment of a molecule's performance divorced from the judgement of those closest to the compounds. In the same way that in software development "with enough eyeballs all bugs are shallow" the open nature of the research makes the science faster. This was found to be the case in a previous open source synthetic chemistry project involving the drug praziquantel.

Experimental Progress to Date


The first series to be tried was based on an arylpyrrole that was one of the most attractive hits in the original GSK dataset. Ultimately this series was parked because the ester, which was metabolically unstable, could not be replaced with another functional group. A related set of compounds, the "Near Neighbours" displayed high potency but were found to be too insoluble. Series 2, the triazoloureas, appeared promising but there was a suggestion another team were working on this series, so it was parked. Series 3, the aminothienopyrimidines, are under current investigation, though the analogs examined to date have been inactive and also suffer from low solubility. It is likely that the project will shortly (end 2013) move to Series 4.

The compounds evaluated to date (assigned OSM codes) can be viewed: picture list, .sdf, old spreadsheet. The first 100 compounds were uploaded to ChEMBL.

General Strategies

How to Obtain Other Compounds

Many of the original compounds from the 2010 GSK screen arose from libraries purchased from smaller specialised companies. How best to obtain analogs of hits in the OSM project? Novel compounds clearly need to be synthesised. Other compounds may be available by other means, however.

1) Identification of Relevant Commercial Compounds: What if some relevant compounds are already commercially available? How can these be found? Iain Wallace was able to do a search of databases such as eMolecules for relevant compounds above a certain threshold of similarity and filter compounds by supplier, generating a "hitlist" quickly and with no manual human input. These can be converted into spreadhseets for quick visualisation - see here for examples in the aminothienopyrimidine series.

2) Obtaining Commercial Compounds: With the compounds identified, the relevant suppliers need to be contacted to ask for donations. That will probably not be trivial since it needs a human interaction. Failing that the compounds can just be bought.

3) Identification of Other/Academic Compounds: What about desirable, known compounds that are not commercially available, e.g. compounds sitting in academic lab fridges? Some of these may be identified using resources like SciFinder, though these require expensive subscriptions. Many useful compounds may not even be in the published literature (an argument for openness in science). There are some reports of activity of compounds in Series 1 (e.g., here), though it is not clear whether the activity is relevant to malaria.

4) Get Other/Academic Compounds: This will be a case of manual contact with interested groups. Here is an example enquiry. Naturally contributions are rewarded by possible authorship on resulting papers. Ultimately we (the scientific community) are not efficient at sharing chemical resources. A user-driven list would be helpful that permits the following open appeal: "I need compound X. I can buy it from you, or you can give it to me, or you can make it for me or with me, but I need the compound in timeframe Y." This is like a Molecular Craigslist, and would reduce some of the supply-demand barriers in chemical research.

How to Comment on What You're Reading

Comments/input/questions can be contributed via Google+ either by "+"-ing the project or in the Open Source Malaria Research Community, directly on the relevant Electronic Lab Notebooks, via Twitter, Facebook or by posting a new Issue to the GitHub To Do list. Much of the older project activity happened on the malaria pages of The Synaptic Leap. The page you're reading also has a "talk" tab for input if you would prefer, though there are no notifications active. Alternatively please write your own input somewhere (e.g., your own blog) and link to the project. Anonymity is perfectly acceptable, just less useful. Please avoid email if you can.

For the full summary of ways to join/interact/contribute, please see the "Join the Team" sheet on the OSM Landing Page.


The project's licence unless otherwise stated is CC-BY-3.0 meaning you can use whatever you want for whatever purpose, provided you cite the project.