-
Notifications
You must be signed in to change notification settings - Fork 6
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
Mur Ligase the Christmas Present Meeting December 2022 #92
Comments
Hi all - I'm going to be late to today's meeting. Please start without me @Yuhang-CADD @chrisdowson1 @LauraDS1 |
Progress: I am currently working on the synthesis of oxadiazole (conversion of the bromine to an amine using Gabriel's synthesis). Commonly, the yield obtained in this step is low and I might try other methodologies to convert the Br to NH2, for example using the reduction of the azide. For the imidazole fragment: I needed to change the strategy to synthesize it again. The imidazole amine was very polar. I got 4 spots in TLC. All purified and analyzed by NMR, intermediate still impure. Not sure if that is the compound. I decided to start the synthesis protecting the imidazole with Boc, I purchased the amine boronic acid and I am waiting for delivery. |
I've spoken with @yiwei905, and she has done some retrosynthesis searches for other sets of compounds. I will work on AW9 and J06 too. For J06, I've found a Tetrahedron paper that might work for the synthesis of tetrazole aniline. I will try that. |
Date: Dec 13th 2022
Time: 2pm UK time other timezones
Place: https://ucl.zoom.us/j/91379419977
Recording: https://youtu.be/LsM_xhTYAtg
Previous Meeting: #91
Who can come?: Anyone. No need to say anything unless you'd like to.
Apologies: @mattodd late arrival
Decks: Please @opensourceantibiotics/murligase remember that if you share slides/info, to drag and drop those into a comment on this page, below. Very easy and saves @mattodd having to pester you.
Agenda:
Key things today are
i) Multi-targeting compounds identified from Warwick and Atomwise collections. We need a crystal structure of one or more of these multi-targeting hits to pursue grant funding.
ii) Yuhang's "efflux-proof" amine derivative of the AZ compound was found to bind. Does it inhibit MurC?
iii) Is the rest of the Warwick Enamine collection scheduled for evaluation in the enzymatic assay?
(please add if you'd like to prioritise anything)
1) Multi-targeting Compounds from the Warwick/NEU Enamine Collection
2) Multi-targeting Elaborated Fragments from Diamond Fragment Screen
3) Atomwise Hits
@LauraDS1 is waiting for a new sensor type to redo SPR experiments (MurC, MurD in presence and absence of ADP/AMPPNP) on Atomwise compounds (SPR for mur ligases #55 and on [wiki, following the previous crystal structures of several compounds bound(see also Last XChem EcMurE results uploaded #52). To Do: these data need to be cross-checked with the new inhibition data presented by @AJLloyd105 slides to see if we have any X-ray structures of these inhibitors. Note that in the initial screen by @AJLloyd105, 15 of the compounds interfered with the coupling enzymes. 14 of those also interfered with an alternative assay (which is...?), but one did not, and has been added to the list of compounds found to be inhibitors in the Atomwise set.
@yiwei905 to synthesise AW53. Yiwei has started to pursue this compound because it has poor numbers of analogs commercially available. The compound appears to inhibit MurC (Pae), MurD (Eco) and MurE (Eco), which should be checked and explored.
4) Variants of AZ Compounds
5) New Protein Structures
The PDB list has been updated with the new, recent structures: 8EGM, 8EGN, 8DOF, 8DP2, 8EWA. Jan Abendroth has completed the final SSGCID X-ray collection for MurC, with the series of three AZ compounds bound to this protein. In the two protein chains, the piperidine moiety of the ligand is in two different conformations. Jan's assumption is that the conformation in chain B is the native one, since it does not involve interaction with a symmetry mate. Thank you Jan!
6) De Novo Computational Modelling
@AJLloyd105 reported that the competition compounds had been screened vs. Pae MurD enzymatically. High levels of inhibition were observed, but the compounds all also interfered with the coupling enzymes used in the assay, unfortunately. Solutions: 1) reduce the concentration of the test compounds to find a window where the assay works, or 2) find a different assay. @AJLloyd105 to update. In this meeting Should be fine to not worry about off-target effects for now but should be aware that things aren't 100% specific and shouldn't assume they would be.
7) Other Potential Starting Points
8) Misc/AOB
Last time @AJLloyd105 reported on the evaluation, enzymatically, of "double-headed" compounds containing uridine and ATP binders: . These were found to be binders and will be investigated further (need to upload deck). @AJLloyd105 to update as appropriate.
9) List of any Raw Data That Needs Posting Online
Suitable locations: ideally an electronic lab notebook, another suitable repository (Zenodo, Figshare) or Github itself.
9) Mothballs (if no actions then these need to be linked in wiki and closed)
Next Meeting
Jan 10th 2pm UK time
L'esprit de l'escalier
If you'd like to follow up after the meeting, please comment below. You can also email, but please be clear if anything in the email should not be public domain - the default is always open.
The text was updated successfully, but these errors were encountered: