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Mur Ligase Meeting September 2023  #102

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Yuhang-CADD opened this issue Sep 8, 2023 · 10 comments
Open
31 tasks

Mur Ligase Meeting September 2023  #102

Yuhang-CADD opened this issue Sep 8, 2023 · 10 comments
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@mattodd
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@Yuhang-CADD
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Yuhang-CADD commented Sep 8, 2023 •
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Date: Sep 12th 2023
Time: 2pm UK time other timezones

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

Recording: https://youtu.be/XrB8R_32bB0?si=ySufgClfVFvOCbkZ

Previous Meeting: #101
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. 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 by SPR, but gave no activity vs wt bacteria (data on wiki and a summary of data in #96. Need to complete checks of enzymatic activity of these compounds, to verify the design is OK in terms of enzyme inhibition. (Still awaiting for the IC50 values)

iii) When would the rest of the Warwick Enamine collection be scheduled for evaluation in the enzymatic assay?

iv) Shall we suggest a booking & tracking system where people can book period slots for fresh sample testing (easy to arrange shipment and avoid sample deterioration) and see the results remotely in real time? (e.g., we could set it up on google sheet as a live document.)

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

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

  • @AJLloyd105 @chrisdowson1 to update on further enzymatic screening of the Warwick Enamine Collection, following discovery of the hits shown here.
  • @LauraDS1 to update on any soaking and/or co-crystallisation experiments with Warwick Enamine Collection compounds, following (last update here. Previously @LauraDS1 reported that hits had been found for these compounds by SPR, @LauraDS1 to update. Question: Do we have anywhere a comparison of the hits from SPR vs the hits from enzymatic screening? Would be useful. Important update: crystallisation trials for compound J06 (Z2010503124), which has in Laura's hands given: P. aeruginosa MurD IC50 = 16.6 uM; P. aeruginosa MurE IC50 = 12.4 uM; E. coli MurD IC50 = 2.5 uM; E. coli MurE IC50 = 41 uM. @eyermanncj has suggested trying crystallography with this compound with any murC isozymes SSGCID has access to, and murC and murE ADP or ATP structures would we worth trying to get. @LauraDS1 updated last time that E. coli MurD and MurE crystals were being used for soaking and co-cryst experiments. A new crystal was obtained of MurD with compound J06, which was sent to Diamond. Subsequently by email Laura said that there was no diffraction. Ultimately it was felt that E. coli is not working very well as a soaking system, with the compounds "spat out".

Crystallography at The University of Kansas: J06 (Z2010503124) had also been sent to Uni Kansas (Scott Lovell, via Bart).

  • Bart to send J06 for trials (vs what?).

2) Multi-targeting Elaborated Fragments from Diamond Fragment Screen

3) Atomwise Hits

4) Variants of AZ Compounds

  • @AJLloyd105 @LauraDS1 to report on enzymatic inhibition data for amine derivatve of AZ5595, which had shown good SPR binding data here. Any promising compounds (SPR + enzymatic) --> SSGCID. @Rebecca-Steventon may also have evaluated one of @Yuhang-CADD 's compounds (which?) here.
  • @mattodd to reach out to groups that may be happy to run accumulation assays, both on the AZ amine and more generally on new compounds made e.g. Hergenrother lab (e.g. student Rebecca Ulrich), Helen Zgurskaya (Oklahoma).
  • @Yuhang-CADD to update on the Piramal synthesis of key synthetic intermediate.

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!

  • @mattodd to organise new soak-in meeting to consult on structural biology learnings. This meeting was held on Nov 22nd 2022. Outcomes:

6) De Novo Computational Modelling

  • @edwintse to update the synthesis of molecules suggested in Predictive Modelling Competition July Summary #85. The progress was last updated in Mur Ligase the Christmas Present Meeting December 2022 #92.
  • Last time @LauraDS1 updated on the SPR screen of the competition compounds (Predictive Modelling Competition July Summary #85), data summarised here. These data are complete (repeats already done). There are some hits at 100 uM, and one at about 10 uM, which is exciting. Some compounds gave non-specific binding (straight line SPR curve). Obviously no info on where the compounds are binding. Data need adding/linking to the wiki. Next: variants of this SPR-binding compound?
  • @LauraDS1 to evaluate the competition compounds in a crystal soaking assay.
    @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 previous meeting, @AJLloyd105 had evaluated the compounds with a spectrophotometric assay. There is confidence in inhibition arising from OSA-001110 and an IC50 will be generated. Compound 8 also still probably good and will be pursued.
  • @Yuhang-CADD to report on progress towards @jhjensen2's originally-suggested compounds (last update was here.

7) Other Potential Starting Points

  • @chrisdowson1 to summarise status of LifeArc projects, both the previous collaboration and the more recent fragment screening campaigns (with Peter Coombs). Data for the latter has been transferred to Warwick. @mattodd to clarify that all parties are happy for the data to be released into the public domain. @mattodd awaiting reply.
  • Assuming above OK, update to be presented by someone from the Warwick team on enzymatic testing of the LifeArc fragments (which were discovered via an SPR screen). No structural information yet.
  • @chrisdowson1 to report on progress towards securing the Merck Open Global Health Library.

8) CC4CARB Proposal (#93)

Following discussions between @eyermanncj @Yuhang-CADD and @mattodd a proposal is being written for CC4CARBfunding to help with chemistry aimed at exploring more potential binding interactions with the Murs, specifically areas where phosphates normally bind.

9) 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.

  • @mattodd to post GRC conference slides somewhere (28 MB...).
  • We need a volunteer to reach out to CC4CARB to assess whether we are suitable for a proposal.

10) List of any Raw Data That Needs Posting Online

Suitable locations: ideally an electronic lab notebook, another suitable repository (Zenodo, Figshare) or Github itself.

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

Next Meeting

Oct 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.
@Yuhang-CADD Yuhang-CADD added the Meetings Meetings label Sep 8, 2023
@yiwei905
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yiwei905 commented Sep 12, 2023 •
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MurE inhibition data for multitargeting hits sent on the 23rd May and 25th July 2023, including synthesised derivatives of compounds AW53 by @yiwei905, AW9 by @EveCarter, as well as derivatives of the multitargeting compounds bought from Enamine, and 2 competition compounds by @edwintse as summarised here.

MurD inhibition data +structures were also attached: P. aeruginosa MurD inhibition.pdf

Screenshot 2023-09-12 at 20 15 14 Screenshot 2023-09-12 at 20 15 26 Screenshot 2023-09-12 at 20 15 37 Screenshot 2023-09-12 at 20 15 52

P. aeruginosa MurE Inhibition Data of Multitargeting Hits.pdf
P. aeruginosa MurE Inhibition Data of Multitargeting Hits.docx

P. aeruginosa MurD inhibition data.docx

@bartrum
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bartrum commented Sep 12, 2023 via email

@Yuhang-CADD
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Yuhang-CADD commented Sep 12, 2023 •
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1. Amine Building Block (Synthetic Explorations)
Screenshot 2023-09-12 at 13 59 45

2. Guanidinium Reagent Synthesis
Screenshot 2023-09-12 at 13 58 11

@AJLloyd105
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230823 to 080923 data compilation Yiwei OSA MurD E Cand F data 2.pptx

@AJLloyd105
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Dear All,
Please find attached screening data vs P. aeruginosa MurC, D, E and F for Yiwei's OSA (Atomwise and related) compounds sent 230523 and 250723 (previous comment).

@mattodd mattodd reopened this Sep 18, 2023
@mattodd
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mattodd commented Sep 19, 2023

Very good multitargeting data on these compounds, wow.

@phraenquex
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Indeed... terrific!

@phraenquex
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@mattodd if these are structurally related, is it time to do an extensive SAR scan? Warren (@Waztom) has his CAR system working increasingly smoothly, they put 500 crudes into crystals last month; so if these MurCDEF assays can be set up to run as panel, it seems it's worth a try?
Because presumably the challenge of getting to Real Potency for all will need a Lot Of Data, Quickly.

@chrisdowson1
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chrisdowson1 commented Sep 19, 2023 via email

@AJLloyd105
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From the multi-targeting perspective, there are a couple of interesting papers that came out in 2006 and 2007 from the Infectious Diseases Division of Wyeth (before it was phagocytosed by Pfizer). The papers relate to a series of compounds based upon pulvinone. These compounds had activity vs E. coli MurA, B, C and D with IC50 values (quoted in ug/ml but recalculated as uM) of 2.25, 2.25, 4.5 and 13.5 uM (recalculated from Antane et al. (2006). Bioorg Chem Lett, 16, 176-180). The 2007 paper (Mansour et al (2007) ChemMedChem 2, 1414-1417) followed this up, with a crystal structure of one of these molecules in the active site of E. coli MurB ((PDB 2Q85) where the compound was in the substrate binding site) and MIC data, which showed activity vs S. aureus (4 to 64 ug/ml depending on compound) and E. coli (2 to 16 ug/ml), exciting although enthusiasm is curbed a bit on excavation of the text to reveal the E. coli strain (unrecorded) was “outer-membrane permeable”).
The point I am trying to get to, is that as with the pulvinone molecules that may well be recognised for targeting the uridine binding site of MurA to D, I am wondering if the compounds I have found to have MurC to F activity might by analogy be active vs MurB? This conjecture is somewhat encouraged by the fact that (as I am given to understand) the Atomwise compound set and derivatives thereof do not target the ATP pocket of Mur ligases. It’s an easy albeit time-consuming experiment.
Antane et al (2006) Bioorg Med Chem Lett 16, 176-180.pdf
Mansour et al (2007) ChemMedCHem 2, 1414-1417.pdf

@Yuhang-CADD Yuhang-CADD mentioned this issue Oct 6, 2023
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@mattodd mattodd mentioned this issue Nov 26, 2023
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