Mur Ligase Meeting July-August 2024

Yuhang-CADD commented 2 months ago

Date: July 9th 2024 & Aug 13th 2024 Time: 2pm UK time other timezones

Place: https://ucl.zoom.us/j/91379419977

Recording:
Jul: https://www.youtube.com/watch?v=084oK1PiXHA&list=PL0eLxnHhou_k1Upbn5X1mdHBwKMYkRpLH Aug: https://ucl.zoom.us/rec/share/WssF3nz4UgQ_E2Uak0tPJGvvQlfidQB7GyLDOeBZQrdJKr885mDLQENS-bo3Skf4.GZKadnkHNGjm6NyC code: S74=UuP9

Previous Meeting: #111 Who can come?: Anyone. No need to say anything unless you'd like to.

Apologies:

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. Updates on any new IC50 or crystallographic or microbiology data.

ii) New data from Warwick on the contributed AZ compounds (retest at a lower concentration).

iii) Update on crystallographic data of AZ compound 4 (WYH9 compound) in Pae MurD ligase.

(please add if you'd like to prioritise anything)

1) Multi-targeting Compounds from the Warwick/NEU Enamine Collection and Atomwise Compounds

[ ] @AJLloyd105 to update on further enzymatic screening of compounds from the Warwick Enamine Collection and Atomwise libraries, following discovery of the hits shown here.
[ ] @LauraDS1 to update on any soaking and/or co-crystallisation experiments with these compounds, following (last update here. Update on crystallography trials at The University of Kansas (Scott Lovell, via @bartrum): Compound J06 (Z2010503124).
[ ] @gfsfernandes to update on current research in design of improved binders vs TB murs. Note - new repository for this project at https://github.com/opensourceantibiotics/Series3-TB_MurLigase. In last meeting, @AJLloyd105 had tested the first batch of compounds from @gfsfernandes vs MurE. There was some inhibition of the coupled biochemical assay. High concentrations were needed, which raises queries about solubility (which should be measured for these compounds). Another assay was employed, with methylthioguanosine. We probably need SPR, or something else biophysical, though ADP-glo is also possible. Several compounds gave some evidence of inhibition (e.g. GF-62) and IC50s will be measured. It is possible that aggregation may also be affecting these compounds (@loriferrins shared https://www.ncbi.nlm.nih.gov/books/NBK442297/).
[ ] In the last meeting @loriferrins and team (Sam Spijkers-Shaw, Thomas ("Tommy") Waltz-Chesnaye and Cole Iannuzzi (taking over from Tommy) reported. Compounds to be shipped to Warwick then AZ.

2) Multi-targeting Elaborated Fragments from Diamond Fragment Screen

[ ] @LauraDS1 to update on screening (inhibition, SPR, soak) of elaborated Diamond fragments sent by @edwintse in #84.

3) Variants of AZ Compounds

These will include guanidinium and pyridinium derivatives to try to combat efflux.

[ ] @Yuhang-CADD's 1st batch of fresh samples of AZ5595 and derivatives (Alcohols & Amines) need complete data from @AJLloyd105
[ ] @Yuhang-CADD's 2nd batch of fresh samples of AZ5595 and derivatives (Amines & Guanidiniums) need complete data from @AJLloyd105
[ ] @Yuhang-CADD's 3rd batch of fresh samples of AZ5595 and derivatives (Rigid Small Amines & Guanidiniums & Pyridiniums) in progress.
[ ] Accumulation assay - @mattodd to reach out to the Hergenrother lab to see whether accumulation can be measured. Paul Hergenrother helpfuly replied with a contact at Duke who can run this, and @mattodd will follow up.

4) New Protein Structures

No new structures to add to the PDB list.

5) De Novo Computational Modelling

[ ] @mattodd to organise what is known of the competition compounds and what is needed to write the work up for publication.

@Yuhang-CADD has paused synthesis of @jhjensen2's originally-suggested compounds (last update was here while the AZ derivatives are being made.

6) CC4CARB Proposal (#93)

[ ] Successful! Meeting up with committee Aug 6th to plan next steps.

7) 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.

8) Mothballs (if no actions then these need to be linked in wiki and closed)

@mattodd is in the process of converting old items to the wiki

Next Meeting

Aug 13th 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.

Yuhang-CADD commented 2 months ago

Progress Report:

Further Plan on the Structure:

to rule out the potential steric clashes of the southwest side of the AZ structure with MurC in the central domain, might help explain the potency drop of the series of AZ5595 amine and guanidinium derivatives, see data in the slides below:

Warwick open source contribution 090724.pptx

lferrins commented 2 months ago

Northeastern contribution, presented by Cole Iannuzzi. Mur Ligase.pptx

mattodd commented 2 months ago

Notes from today:

1) @AJLloyd105 presented data from the deck above. The data clearly shows that the AZ compounds are effective against MurC but are not multi-targeting. If the guanadinium compound WYH-76-1-P can be included in any MIC assessments, that would be very good. @Yuhang-CADD to incorporate these data into the table in the draft paper and clarify what data remain to be obtained.

2) Scott Lovell (University of Kansas) is working on soaks: Pae MurC in complex with compound F09 - 3A but not great and no density for the compound. Ditto with Pae MurD with compound M02. Compound A19 binds, but to the surface (is that still potentially useful?). Scott was asking whether we want to soak any other more tightly-bound compounds. The answer is yes, if there is an AZ compound for which we have no structure, but the priority remains getting a structure for a compound from a non-AZ series, towards something that is multi-targeting. @LauraDS1 and @AJLloyd105 recommended trying full length protein rather than truncated, even though harder.

3) @mattodd is pursuing accumulation assay and kinetic solubility assays. Solubility assays are widely available though quite expensive, and we are seeking an alternative solution. Accumulation: @mattodd in touch with Hergenrother's lab and will report back.

4) @LauraDS1 is trying cryo-EM later in July and will report back. Apo first, then with any known binders.

5) The NEU team (Cole Iannuzzi) reported on latest synthesis and next shipment - deck posted above.

6) Next meeting - to be detemined whether it should go ahead, given summer.

AJLloyd105 commented 1 month ago

Hi, I've updated the presentation I showed (Warwick open source contribution 090724.pptx) by including the replots of data required to extract the Ki values that were included in this presentation. This version is Warwick open source contribution 090724-3.pptx Adrian (@AJLloyd105) Warwick open source contribution 090724-3.pptx

Yuhang-CADD commented 1 month ago

Further Progress

Have obtained the following structures over the past two weeks through HPLC purifications. Awaiting NMR and HRMS to further confirm some of the structures.

AJLloyd105 commented 1 month ago

Hi, Great! When are you looking to ship? Best Wishes, Adrian

From: Yuhang Wang @.> Sent: Monday, August 5, 2024 3:25 PM To: opensourceantibiotics/murligase @.> Cc: Lloyd, Adrian @.>; Mention @.> Subject: Re: [opensourceantibiotics/murligase] Mur Ligase Meeting July 2024 (Issue #112)

Further Progress Screenshot.2024-08-05.at.15.24.45.png (view on web)https://github.com/user-attachments/assets/51b53f1e-b485-42b2-bda1-ef1d28acb995

- Reply to this email directly, view it on GitHubhttps://github.com/opensourceantibiotics/murligase/issues/112#issuecomment-2269208201, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AY5MUXDOPRJ2PEB765UFTYDZP6DMZAVCNFSM6AAAAABKNGYCASVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENRZGIYDQMRQGE. You are receiving this because you were mentioned.Message ID: @.**@.>>

Yuhang-CADD commented 3 weeks ago

Brief Summary of Aug Meeting:

Adrian's update on NEU's compounds (IC50s)
NEU's shipment received and ready to ship to Warwick.
Yuhang's compounds ready to ship (50mM in mLs), AZ5595 powder needed
Atomise compounds vs TB, update needed from @gfsfernandes

AJLloyd105 commented 3 weeks ago

Warwick contribution to the August 2024 meeting. Analysis of NEU compounds as P. aeruginosa MurD inhibitors 190724-2.pptx

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