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opensourceantibiotics / murligase

Everything to do with the Mur Ligase Project
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SPR results uploaded #61

Closed LauraDS1 closed 2 years ago

LauraDS1 commented 2 years ago

Hi everyone,

I have uploaded the SPR results. Let me know if there are any questions.

All the best, Laura

LauraDS1 commented 2 years ago

https://github.com/opensourceantibiotics/murligase/wiki/SPR-with-the-Atomwise-library

mattodd commented 2 years ago

This is great! I've taken the files you posted and put them in the main filestore here.

I've also started a new page on the wiki to try to summarise where we're up to with the Atomwise compounds, since I was getting confused. The page you started on the wiki (the one you linked above) was an "orphan" - it wasn't linked to anywhere and didn't appear on the wiki menu, so it would be hard to discover it if you were looking.

@LauraDS1 and @danaklug could you please look at that wiki page and edit it if I've missed anything out. Does it include everything and make sense? If not, please change it.

@LauraDS1 it's great you did these experiments. So, four compounds showed binding competitive with AMPPCP?

LauraDS1 commented 2 years ago

Thanks a lot @mattodd! I was trying to link the results but it was not letting me.

After finding hits binding in the new pocket, we rose the question whether they would still be binding in the presence of ATP. In the SPR experiment in the presence of the ATP analogue, under the tested conditions, those four XChem hits seem to be able to bind. Therefore, this new pocket might be able to form in the presence of ATP. I have not been able to do the dose response experiments with AMPPCP, so we won't know if the binding would be in the same KD range than in the absence of AMPPCP.

mattodd commented 2 years ago

@LauraDS1 so do we know if the binding of the Atomwise compounds is competing with ATP or binding in another pocket? Or can't we say?

LauraDS1 commented 2 years ago

@mattodd We know the Atomwise compounds that were XChem hits bind in a different pocket. The other compounds, I can't confirm that at this point. I would need to run a dose response experiment with all the hits. Also, I think we need to have activity assay data so we can correlated the SPR experiment results with activity.

The AW compound that gave a negative binding curve, like the AMPPCP, did't show binding in the presence of AMPPCP. Therefore, I wonder if having a negative binding signal on SPR for these proteins means it is an ATP site binder. I would like to see if the activity assay confirms this theory or not.