Experimental identification of target for Series 3

[holeung]

I received a small grant to support experimental, biochemical testing of potential targets for Series 3 (#549) through partnerships with the wonderful core labs (NMR, mass spectrometry, X-ray crystallography, protein expression) of the University of Kansas.

Current approaches that we discussed include:

1. Recombinant expression of candidate kinase/kinase-like targets as discussed in #549. We would prefer to start with those with published expression protocols and that can be expressed in E. coli. We would test for inhibitor binding by saturation transfer difference NMR. We would start by testing our top 5 candidates.

2. Screening of inhibitors against fractions of Plasmodium lysate or enriched lysate, preferably from a non-infectious Plasmodium species or sterilized P. falciparum. We would screen by STD NMR, affinity mass spectrometry, or by something like DARTS (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4442491/). Anyone know of a source of Plasmodium lysate?

3. Your idea here! Note that target identification is considered difficult and non-routine.

I will keep this sub-project open and under the umbrella and spirit of OSM.

[MFernflower]

@drc007 @mbhebhe Do you think it would be worth making this just to see how much of a role CA blockade plays in the activity of the S3 drugs? (Possible alongside dorzolamide)

[drc007]

Since we don't know activity at CA, and we don't know which (if any) kinase might be involved or the activity, I don't think you would be able to interpret any results.

[drc007]

Thanks @mpollastri I suspected as much but did not want to skew the discussion.

If selectivity is the primary issue then it needs to be addressed up front. There are plenty of known carbonic anhydrase inhibitors in the literature that could be used in any experiments.

The key experiment would be something along the lines of taking a known CA inhibitor with measured activities at both human and parasite carbonic anhydrase. Then running an in vivo experiment to find the plasma concentrations at trough that are required for complete elimination of the parasite (not ID50). We also need to know the peak plasma concentrations after oral dosing at the efficacious dose.

We can then try to predict the likely inhibition of the human CA that might be seen a peak plasma concentrations and whether this would be an issue. Hopefully we can then calculate what level of selectivity is required in a potential drug. We can then look at whether the level of selectivity is realistic before we commit any chemistry resources.

[drc007]

Given the above discussion I've been looking at the series 3 compounds. OSM-S- (IC50 0.2 uM) is a puzzle. According to the structure in the spreadsheet shown below, this does not contain a sulphone. I suspect that this structure is incorrect, can we check?

[MFernflower]

^^^^ If that structure is accurate and is really able to kill at 200 nanomolar - what on earth could it be targeting? It looks super strange - almost like a ROCK inhibitor https://en.m.wikipedia.org/wiki/Rho_kinase_inhibitor

[MFernflower]

I feel we aught to at some point spin off the suspected CA inhibition to a issue in the s3 repo - things are getting super tangled especially with the s3 hit possibly being promiscuous! @drc007 since you seem more experienced with carbonic anhydrase could you open the issue? (When time permits ofcourse)

[mbhebhe]

Its actually TCMDC-134392. Its a GSK compound and it doesn't have an OSM number. But it does have an activity value of 0.23 uM

[david1597]

It has been assigned OSM-S-590.

[drc007]

Sure it is not http://www.chemspider.com/Chemical-Structure.24574288.html

[holeung]

Yes, I would also be interested to know if the Series 3 compounds block carbonic anhydrase.

[drc007]

I've written a comparison of several bioactivity prediction packages. https://www.macinchem.org/reviews/bioactivities/bioactivities.php

I included OSM-S-106 as a test compound, unsurprisingly Carbonic Anhydrase inhibition and a variety of kinase targets are flagged.

[MFernflower]

@drc007 here is another free service that could be worth testing http://www.swisstargetprediction.ch/

On Tue, Jan 22, 2019, 2:53 PM Chris Swain <notifications@github.com wrote:

I've written a comparison of several bioactivity prediction packages. https://www.macinchem.org/reviews/bioactivities/bioactivities.php

I included OSM-S-106 as a test compound, unsurprisingly Carbonic Anhydrase inhibition and a variety of kinase targets are flagged.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/OpenSourceMalaria/OSM_To_Do_List/issues/561#issuecomment-456539324, or mute the thread https://github.com/notifications/unsubscribe-auth/ADBLDiAtQULjeKZASaVi07H0QFtzCCt3ks5vF2wegaJpZM4SZ3Um .

[drc007]

@MFernflower That uses pretty old version of ChEMBL (v16) and I don't think it as been updated since 2103?

[MFernflower]

@drc007 that could explain why it sometimes returns screwy results PBB2 seems much more reliable