Mur Ligase Halloweener Meeting October 2022

[mattodd]

Date: Oct 11th 2022
Time: 2pm UK time (other times)
Place: https://ucl.zoom.us/j/91379419977
Recording: https://youtu.be/7T2ZC-moghQ
Previous Meeting: #88
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) Follow-up screening of multi-targeting compounds from Warwick and Atomwise collections
ii) Do we need Soak-In Follow Up (this was mentioned in the original #80).
(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.
• @eyermanncj @LauraDS1 to update on any additional near-neighbour compounds that have consequently been ordered/evaluated. @edwintse has posted on this in Enamine/Atomwise Multitargeting Hits - Nearest Neighbours #89. Following this analysis it was decided in meeting that @edwintse and @mattodd would propose purchase of some compounds related to the Warwick and Atomwise collections - there is grant money available for this that needs to be spent before January. There was a high confidence in the group that the hits identified are "real".
• @LauraDS1 to update on any soaking and/or co-crystallisation experiments with these compounds (last update here). In meeting: @LauraDS1 reported that the analysis of the Enamine compounds by SPR was underway (hits have been found!), with results expected imminently. As things stand, there appears to be no correlation between hits observed by SPR and hits observed by enzymatic screening. See also below for comments on the use of an alternative assay for the Atomwise compounds.

2) Multi-targeting Elaborated Fragments from Diamond Fragment Screen

• @LauraDS1 to update on screening (inhibition, SPR, soak) of elaborated fragments sent by @edwintse in Compound to Warwick Inhibition Assay Jun 2022 #84.

3) Atomwise Hits

• @LauraDS1 to complete 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. In meeting: 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.
• Residual item to do: @LauraDS1 @LizbeK to clarify, on the wiki here, whether the Atomwise compounds that have been co-crystallised have a binding site that overlaps with the "target site" Atomwise used @LauraDS1 addressed this here and in the March meeting there was discussion that the Atomwise compounds did bind in a partial overlap with the intended binding site. This has been clarified as part of Predictive Modelling Competition to Design Binders of MurD, an Antibacterial Target #69, and all we need now is @LauraDS1 to summarise briefly on wiki what we know.
• Based on the above, and the near neighbours identified by @edwintse, @mattodd to follow up with Denzil Bernard about potential additional suggestions from Atomwise. Note that we're being asked for this: "I have attached your data reporting form that will help us interpret your results. The form is organized by plate location and tube barcode, so please check to ensure that the tube barcode matches the reported results. Feel free to modify the form to fit your experiment" where the relevant spreadsheet is here, screenshot below.

4) Variants of AZ Compounds

• @Yuhang-CADD to update on the shipping of AZ5595 and the amino derivative of that compound (OSA_001095). In meeting: @Yuhang-CADD's amine compound is likely to be the formate salt, which should be factored into the molecular weight calculation. @Yuhang-CADD to confirm with @LauraDS1.
• @Yuhang-CADD to consider which proteins we should ask SSGCID to crystallise with these compounds, if activity is found at Warwick - involves checking whether the compounds have given any inhibition vs Murs other than MurC, and what we want to know with these compounds.
• @Yuhang-CADD to prioritise the completion of the synthesis of the amino derivative of AZ5595.
• @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).
• @Rebecca-Steventon to report on the assay @Yuhang-CADD 's compound (which?) here.
• @chrisdowson1 to work on compound transfer from SSGCID to Warwick and update the group. Does this need an update, or can it be mothballed?

5) New Protein Structures

Last time Jan Abendroth updated us that new structures were deposited:

Pseudomonas MurC with AZ13644908, PDB code 8egm
Pseudomonas MurC with AZ13643701, PDB code 8egn

(More data on these:
PDB ID: 8EGM
Structure deposited on: 09/12/2022
SSGCID PROTEIN ID: PsaeA.00137.b.B5.PW37941
Ligand(s): AZ13644908
Structure of:UDP-N-acetylmuramate--L-alanine ligase (EC 6.3.2.8) (UDP-N-acetylmuramoyl-L-alanine synthetase)
From: Pseudomonas aeruginosa
SSGCID gene/pathway page: http://apps.sbri.org/SSGCIDTargetStatus/Target/PsaeA.00137.b

PDB ID: 8EGN
Structure deposited on: 09/12/2022
SSGCID PROTEIN ID: PsaeA.00137.b.B5.PW37941
Ligand(s): AZ13643701
Structure of:UDP-N-acetylmuramate--L-alanine ligase (EC 6.3.2.8) (UDP-N-acetylmuramoyl-L-alanine synthetase)
From: Pseudomonas aeruginosa
SSGCID gene/pathway page: http://apps.sbri.org/SSGCIDTargetStatus/Target/PsaeA.00137.b)

These are the AZ compounds that are the ligands here:

Recent structure deposited for Pae MurD with UMA bound, PDB ID: 8DP2 needs collating together with other structures in wiki page (maybe this one?) or in #67. Volunteer to collect all structures? Also add the new structure of Pae MurC with OSA_001044 bound, PDB ID: 8DOF (https://doi.org/10.2210/pdb8DOF/pdb).

Additional email update from Jan Abendroth (11/10/22):
"With trays that had been set up before the end of the UCB involvement with SSGCID I could get collect a final SSGCID X-ray data set for MurC with compound AZ-13644923 during our APS shift last Thursday. Curiously enough, the variable region of the ligand shows up in two conformations. In chain B, the morpholine ring is well ordered and in the conformation shown below. In chain A, the ring is less ordered with rather weak density, however, it clearly points towards a crystallographic mate. The very thin lines depict this. I think that the conformation in chain B is the relevant one. I will finish up the structure soon and share it with the group once peer-reviewed. I can present in one of the upcoming meetings, though not tomorrow. Glad to finish off this series of ligands with a nice structure."

Thank you Jan!

A discussion of the possible value of truncated structures was had as part of the Soak-In at #80. <-- any conclusions we can summarise? New Soak-in meeting will be organised by @mattodd

6) De Novo Computational Modelling

• @edwintse @danielgedder to complete synthesis/procurement of molecules suggested in Predictive Modelling Competition July Summary #85.
• @LauraDS1 to book an SPR screen in the last week in August (week of 29th?). In meeting: @LauraDS1 updated on the analysis of the competition compounds (Predictive Modelling Competition July Summary #85) by SPR. Data summarised here. The 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.
• @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.
• @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) Misc/AOB

In meeting: @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).

• @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.

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.

• @Rebecca-Steventon - dose-response data for potential dual inhibitors OSA742, OSA754, OSA759, OSA789 that was summarised in this graphic.

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

• @Rebecca-Steventon has posted data of @LizbeK fragment screen (https://github.com/opensourceantibiotics/murligase/wiki/Pocket-binding-site - but @drc007 would like structures to be added).
• @LauraDS1 to liaise with Peter and @LizbeK to see if a soak of the @eyermanncj Enamine compounds is possible at Diamond.
• Comparative analysis was done by @ZigBu of mur ligase ATP binding sites (Comparison of the ATP Sites/Structural Similarity Between Murs #56). Any learnings?
• @ZigBu also posted (UCL Mur Ligase Local Team Meetings November 2021  #57) on a paper highlighting that mur domain movement may not be dependent on substrate binding. Again, anything we need to consider? @eyermanncj posted "As a reminder the dynamics of E. coli murD is well established. Here is a “recent” NMR study on E. coli murD."
• @mattodd @chrisdowson1 have parked the idea of a Euro Lead Factory screen.
• Do we need to consider the importance of the observed carbamoylation of a residue (Lys198 (-> KCX198) in a structure (7TI7). Does this influence inhibitor design? See @eyermanncj's analysis
• @eyermanncj and @chrisdowson1 to speak to the benefits of ordering the Enamine kinase library. Should this be mothballed?

Next Meeting

Nov 8th 2pm UK time. The meeting is the Firecracker.

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.

[chrisdowson1]

Mat Apologies – I have a live interview with BBSRC for a Prosperity Partnership award which clashes tomorrow – sorry Adrian Laura and Becca can update as indicated across Enamine, Atomwise and Life Arc compounds Good evidence for multi targeting, some off target activity against coupling enzymes used in the assay will need to balance improved target affinity with multi targeting and permeation into cells Finally need to discuss with systems modelling community at Warwick (cc Neil and Mike) re How much(%) inhibition of how many mur ligases is/are required for effective in vivo inhibition of bacterial growth BW. Chris From: Mat Todd ***@***.***> Date: Monday, 10 October 2022 at 12:52 To: opensourceantibiotics/murligase ***@***.***> Cc: Dowson, Christopher ***@***.***>, Mention ***@***.***> Subject: [opensourceantibiotics/murligase] Mur Ligase Halloweener Meeting October 2022 (Issue #90) Date: Oct 11th 2022 Time: 2pm UK time (other times<https://www.timeanddate.com/worldclock/meetingdetails.html?year=2022&month=10&day=11&hour=13&min=0&sec=0&p1=43&p2=136&p3=37&p4=771&p5=235&p6=152&p7=770&p8=250&p9=196&p10=240>) Place: https://ucl.zoom.us/j/91379419977 Recording: Previous Meeting: #88<#88> Apologies: Decks: Please @opensourceantibiotics/murligase<https://github.com/orgs/opensourceantibiotics/teams/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<https://github.com/mattodd> having to pester you. Agenda: Key things today are i) Follow-up screening of multi-targeting compounds from Warwick and Atomwise collections ii) (please add if you'd like to prioritise anything) 1) Multi-targeting Compounds from the Warwick/NEU Enamine Collection * @AJLloyd105<https://github.com/AJLloyd105> @chrisdowson1<https://github.com/chrisdowson1> to update on further enzymatic screening of the Warwick Enamine Collection, following discovery of the hits shown here<#86 (comment)>. * @eyermanncj<https://github.com/eyermanncj> @LauraDS1<https://github.com/LauraDS1> to update on any additional near-neighbour compounds that have consequently been ordered/evaluated. @edwintse<https://github.com/edwintse> has posted on this in #89<#89> * @LauraDS1<https://github.com/LauraDS1> to update on any soaking and/or co-crystallisation experiments with these compounds (last update here<#87 (comment)>). 2) Multi-targeting Elaborated Fragments from Diamond Fragment Screen * @LauraDS1<https://github.com/LauraDS1> to update on screening (inhibition, SPR, soak) of elaborated fragments sent by @edwintse<https://github.com/edwintse> in #84<#84>. 3) Atomwise Hits * @LauraDS1<https://github.com/LauraDS1> to complete SPR experiments (MurC, MurD in presence and absence of ADP/AMPPNP) on Atomwise compounds (#55<#55> and on wiki<https://github.com/opensourceantibiotics/murligase/wiki/SPR-with-the-Atomwise-library>), following the previous crystal structures of several compounds bound<https://github.com/opensourceantibiotics/murligase/wiki/XChem-EcMurE-Atomwise-library-1> (see also #52<#52>). To Do: these data need to be cross-checked with the new inhibition data presented by @AJLloyd105<https://github.com/AJLloyd105> (slides<https://github.com/opensourceantibiotics/murligase/blob/master/Talks_Meetings_Events/2022%20Sept%20Meeting/Adrian%20Lloyd%20et%20al%20130922%20IV.pptx>) to see if we have any X-ray structures of these inhibitors. * Residual item to do: @LauraDS1<https://github.com/LauraDS1> @LizbeK<https://github.com/LizbeK> to clarify, on the wiki here<https://github.com/opensourceantibiotics/murligase/wiki/XChem-EcMurE-Atomwise-library-1>, whether the Atomwise compounds that have been co-crystallised have a binding site that overlaps with the "target site" Atomwise used<#66 (comment)> @LauraDS1<https://github.com/LauraDS1> addressed this here<#66 (comment)> and in the March meeting there was discussion that the Atomwise compounds did bind in a partial overlap with the intended binding site. This has been clarified as part of #69<#69>, and all we need now is @LauraDS1<https://github.com/LauraDS1> to summarise briefly on wiki what we know. * Based on the above, and the near neighbours identified by @edwintse<https://github.com/edwintse>, @mattodd<https://github.com/mattodd> to follow up with Denzil Bernard about potential additional suggestions from Atomwise. Note that we're being asked for this: "I have attached your data reporting form that will help us interpret your results. The form is organized by plate location and tube barcode, so please check to ensure that the tube barcode matches the reported results. Feel free to modify the form to fit your experiment" where the relevant spreadsheet is here<https://github.com/opensourceantibiotics/murligase/tree/master/Atomwise/Data%20Back%20to%20Atomwise>, screenshot below. [Screenshot 2022-09-13 at 13 35 20]<https://user-images.githubusercontent.com/4386101/189902447-f57ddf96-fa8e-49cc-bdc5-ba569132b0ee.png> 4) Variants of AZ Compounds * @Yuhang-CADD<https://github.com/Yuhang-CADD> to update on the shipping of AZ5595 and the amino derivative of that compound (OSA_001095). * @Yuhang-CADD<https://github.com/Yuhang-CADD> to consider which proteins we should ask SSGCID to crystallise with these compounds, if activity is found at Warwick - involves checking whether the compounds have given any inhibition vs Murs other than MurC, and what we want to know with these compounds. * @Yuhang-CADD<https://github.com/Yuhang-CADD> to prioritise the completion of the synthesis of the amino derivative of AZ5595. * @mattodd<https://github.com/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). * @Rebecca-Steventon<https://github.com/Rebecca-Steventon> to report on the assay @Yuhang-CADD<https://github.com/Yuhang-CADD> 's compound (which?) here<#54 (comment)>. * @chrisdowson1<https://github.com/chrisdowson1> to work on compound transfer from SSGCID to Warwick and update the group. Does this need an update, or can it be mothballed? 5) New Protein Structures Last time Jan Abendroth updated us that new structures were deposited: Pseudomonas MurC with AZ13644908, PDB code 8egm Pseudomonas MurC with AZ13643701, PDB code 8egn (More data on these: PDB ID: 8EGM Structure deposited on: 09/12/2022 SSGCID PROTEIN ID: PsaeA.00137.b.B5.PW37941 Ligand(s): AZ13644908 Structure of:UDP-N-acetylmuramate--L-alanine ligase (EC 6.3.2.8) (UDP-N-acetylmuramoyl-L-alanine synthetase) From: Pseudomonas aeruginosa SSGCID gene/pathway page: http://apps.sbri.org/SSGCIDTargetStatus/Target/PsaeA.00137.b PDB ID: 8EGN Structure deposited on: 09/12/2022 SSGCID PROTEIN ID: PsaeA.00137.b.B5.PW37941 Ligand(s): AZ13643701 Structure of:UDP-N-acetylmuramate--L-alanine ligase (EC 6.3.2.8) (UDP-N-acetylmuramoyl-L-alanine synthetase) From: Pseudomonas aeruginosa SSGCID gene/pathway page: http://apps.sbri.org/SSGCIDTargetStatus/Target/PsaeA.00137.b) These are the AZ compounds that are the ligands here: [https://user-images.githubusercontent.com/4386101/194859586-f79e8d74-d69e-46e2-a9f0-77ff74a17503.png]<https://user-images.githubusercontent.com/4386101/194859586-f79e8d74-d69e-46e2-a9f0-77ff74a17503.png> Recent structure deposited for Pae MurD with UMA bound, PDB ID: 8DP2 needs collating together with other structures in wiki page (maybe this one<https://github.com/opensourceantibiotics/murligase/wiki/PDB-and-Fragalysis>?) or in #67<#67>. Volunteer to collect all structures? Also add the new structure of Pae MurC with OSA_001044 bound, PDB ID: 8DOF (https://doi.org/10.2210/pdb8DOF/pdb). A discussion of the possible value of truncated structures was had as part of the Soak-In at #80<#80>. <-- any conclusions we can summarise? 6) De Novo Computational Modelling * @edwintse<https://github.com/edwintse> @danielgedder<https://github.com/danielgedder> to complete synthesis/procurement of molecules suggested in #85<#85>. * @LauraDS1<https://github.com/LauraDS1> to book an SPR screen in the last week in August (week of 29th?). * @Yuhang-CADD<https://github.com/Yuhang-CADD> to report on progress towards @jhjensen2<https://github.com/jhjensen2>'s originally-suggested compounds (last update was here<#75 (comment)>) 7) Other Potential Starting Points * @chrisdowson1<https://github.com/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<https://github.com/mattodd> to clarify that all parties are happy for the data to be released into the public domain. @mattodd<https://github.com/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<https://github.com/chrisdowson1> to report on progress towards securing the Merck Open Global Health Library<https://www.merckgroup.com/en/research/open-innovation/biopharma-open-innovation-portal/open-global-health-library.html>. 8) Misc/AOB * @mattodd<https://github.com/mattodd> to post GRC conference slides somewhere (28 MB...). * We need a volunteer to reach out to CC4CARB<https://www.cc4carb-collection.org/> to assess whether we are suitable for a proposal. 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. * @Rebecca-Steventon<https://github.com/Rebecca-Steventon> - dose-response data for potential dual inhibitors OSA742, OSA754, OSA759, OSA789 that was summarised in this graphic<#66 (comment)>. 9) Mothballs (if no actions then these need to be linked in wiki and closed) * @Rebecca-Steventon<https://github.com/Rebecca-Steventon> has posted data of @LizbeK<https://github.com/LizbeK> fragment screen (https://github.com/opensourceantibiotics/murligase/wiki/Pocket-binding-site - but @drc007<https://github.com/drc007> would like structures to be added). * @LauraDS1<https://github.com/LauraDS1> to liaise with Peter and @LizbeK<https://github.com/LizbeK> to see if a soak of the @eyermanncj<https://github.com/eyermanncj> Enamine compounds is possible at Diamond. * Comparative analysis was done by @ZigBu<https://github.com/ZigBu> of mur ligase ATP binding sites (#56<#56>). Any learnings? * @ZigBu<https://github.com/ZigBu> also posted (#57<#57>) on a paper<https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0152075> highlighting that mur domain movement may not be dependent on substrate binding. Again, anything we need to consider? @eyermanncj<https://github.com/eyermanncj> posted "As a reminder the dynamics of E. coli murD is well established. Here<https://dx.doi.org/10.1038/srep16685> is a “recent” NMR study on E. coli murD." * @mattodd<https://github.com/mattodd> @chrisdowson1<https://github.com/chrisdowson1> have parked the idea of a Euro Lead Factory screen. * Do we need to consider the importance of the observed carbamoylation of a residue (Lys198 (-> KCX198) in a structure (7TI7). Does this influence inhibitor design? See @eyermanncj<https://github.com/eyermanncj>'s analysis<#67 (comment)> * @eyermanncj<https://github.com/eyermanncj> and @chrisdowson1<https://github.com/chrisdowson1> to speak to the benefits of ordering the Enamine kinase library. Should this be mothballed? Next Meeting Nov 8th 2pm UK time. The meeting is the Firecracker — Reply to this email directly, view it on GitHub<#90>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ALNDKBKNPLV3GPDHYEGSKM3WCP7ITANCNFSM6AAAAAARBIVREM>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[jhjensen2]

Can't make the meeting tomorrow due to travel

[drc007]

Hi, Aplogies I now have a meetings clash. Cheers, Chris

…

On 10 Oct 2022, at 12:50, Mat Todd ***@***.***> wrote: Date: Oct 11th 2022 Time: 2pm UK time (other times <https://www.timeanddate.com/worldclock/meetingdetails.html?year=2022&month=10&day=11&hour=13&min=0&sec=0&p1=43&p2=136&p3=37&p4=771&p5=235&p6=152&p7=770&p8=250&p9=196&p10=240>) Place: https://ucl.zoom.us/j/91379419977 <https://ucl.zoom.us/j/91379419977> Recording: Previous Meeting: #88 <#88> Apologies: Decks: Please @opensourceantibiotics/murligase <https://github.com/orgs/opensourceantibiotics/teams/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 <https://github.com/mattodd> having to pester you. Agenda: Key things today are i) Follow-up screening of multi-targeting compounds from Warwick and Atomwise collections ii) (please add if you'd like to prioritise anything) 1) Multi-targeting Compounds from the Warwick/NEU Enamine Collection @AJLloyd105 <https://github.com/AJLloyd105> @chrisdowson1 <https://github.com/chrisdowson1> to update on further enzymatic screening of the Warwick Enamine Collection, following discovery of the hits shown here <#86 (comment)>. @eyermanncj <https://github.com/eyermanncj> @LauraDS1 <https://github.com/LauraDS1> to update on any additional near-neighbour compounds that have consequently been ordered/evaluated. @edwintse <https://github.com/edwintse> has posted on this in #89 <#89> @LauraDS1 <https://github.com/LauraDS1> to update on any soaking and/or co-crystallisation experiments with these compounds (last update here <#87 (comment)>). 2) Multi-targeting Elaborated Fragments from Diamond Fragment Screen @LauraDS1 <https://github.com/LauraDS1> to update on screening (inhibition, SPR, soak) of elaborated fragments sent by @edwintse <https://github.com/edwintse> in #84 <#84>. 3) Atomwise Hits @LauraDS1 <https://github.com/LauraDS1> to complete SPR experiments (MurC, MurD in presence and absence of ADP/AMPPNP) on Atomwise compounds (#55 <#55> and on wiki <https://github.com/opensourceantibiotics/murligase/wiki/SPR-with-the-Atomwise-library>), following the previous crystal structures of several compounds bound <https://github.com/opensourceantibiotics/murligase/wiki/XChem-EcMurE-Atomwise-library-1> (see also #52 <#52>). To Do: these data need to be cross-checked with the new inhibition data presented by @AJLloyd105 <https://github.com/AJLloyd105> (slides <https://github.com/opensourceantibiotics/murligase/blob/master/Talks_Meetings_Events/2022%20Sept%20Meeting/Adrian%20Lloyd%20et%20al%20130922%20IV.pptx>) to see if we have any X-ray structures of these inhibitors. Residual item to do: @LauraDS1 <https://github.com/LauraDS1> @LizbeK <https://github.com/LizbeK> to clarify, on the wiki here <https://github.com/opensourceantibiotics/murligase/wiki/XChem-EcMurE-Atomwise-library-1>, whether the Atomwise compounds that have been co-crystallised have a binding site that overlaps with the "target site" Atomwise used <#66 (comment)> @LauraDS1 <https://github.com/LauraDS1> addressed this here <#66 (comment)> and in the March meeting there was discussion that the Atomwise compounds did bind in a partial overlap with the intended binding site. This has been clarified as part of #69 <#69>, and all we need now is @LauraDS1 <https://github.com/LauraDS1> to summarise briefly on wiki what we know. Based on the above, and the near neighbours identified by @edwintse <https://github.com/edwintse>, @mattodd <https://github.com/mattodd> to follow up with Denzil Bernard about potential additional suggestions from Atomwise. Note that we're being asked for this: "I have attached your data reporting form that will help us interpret your results. The form is organized by plate location and tube barcode, so please check to ensure that the tube barcode matches the reported results. Feel free to modify the form to fit your experiment" where the relevant spreadsheet is here <https://github.com/opensourceantibiotics/murligase/tree/master/Atomwise/Data%20Back%20to%20Atomwise>, screenshot below. <https://user-images.githubusercontent.com/4386101/189902447-f57ddf96-fa8e-49cc-bdc5-ba569132b0ee.png> 4) Variants of AZ Compounds @Yuhang-CADD <https://github.com/Yuhang-CADD> to update on the shipping of AZ5595 and the amino derivative of that compound (OSA_001095). @Yuhang-CADD <https://github.com/Yuhang-CADD> to consider which proteins we should ask SSGCID to crystallise with these compounds, if activity is found at Warwick - involves checking whether the compounds have given any inhibition vs Murs other than MurC, and what we want to know with these compounds. @Yuhang-CADD <https://github.com/Yuhang-CADD> to prioritise the completion of the synthesis of the amino derivative of AZ5595. @mattodd <https://github.com/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). @Rebecca-Steventon <https://github.com/Rebecca-Steventon> to report on the assay @Yuhang-CADD <https://github.com/Yuhang-CADD> 's compound (which?) here <#54 (comment)>. @chrisdowson1 <https://github.com/chrisdowson1> to work on compound transfer from SSGCID to Warwick and update the group. Does this need an update, or can it be mothballed? 5) New Protein Structures Last time Jan Abendroth updated us that new structures were deposited: Pseudomonas MurC with AZ13644908, PDB code 8egm Pseudomonas MurC with AZ13643701, PDB code 8egn (More data on these: PDB ID: 8EGM Structure deposited on: 09/12/2022 SSGCID PROTEIN ID: PsaeA.00137.b.B5.PW37941 Ligand(s): AZ13644908 Structure of:UDP-N-acetylmuramate--L-alanine ligase (EC 6.3.2.8) (UDP-N-acetylmuramoyl-L-alanine synthetase) From: Pseudomonas aeruginosa SSGCID gene/pathway page: http://apps.sbri.org/SSGCIDTargetStatus/Target/PsaeA.00137.b <http://apps.sbri.org/SSGCIDTargetStatus/Target/PsaeA.00137.b> PDB ID: 8EGN Structure deposited on: 09/12/2022 SSGCID PROTEIN ID: PsaeA.00137.b.B5.PW37941 Ligand(s): AZ13643701 Structure of:UDP-N-acetylmuramate--L-alanine ligase (EC 6.3.2.8) (UDP-N-acetylmuramoyl-L-alanine synthetase) From: Pseudomonas aeruginosa SSGCID gene/pathway page: http://apps.sbri.org/SSGCIDTargetStatus/Target/PsaeA.00137.b <http://apps.sbri.org/SSGCIDTargetStatus/Target/PsaeA.00137.b>) These are the AZ compounds that are the ligands here: <https://user-images.githubusercontent.com/4386101/194859586-f79e8d74-d69e-46e2-a9f0-77ff74a17503.png> Recent structure deposited for Pae MurD with UMA bound, PDB ID: 8DP2 needs collating together with other structures in wiki page (maybe this one <https://github.com/opensourceantibiotics/murligase/wiki/PDB-and-Fragalysis>?) or in #67 <#67>. Volunteer to collect all structures? Also add the new structure of Pae MurC with OSA_001044 bound, PDB ID: 8DOF (https://doi.org/10.2210/pdb8DOF/pdb <https://doi.org/10.2210/pdb8DOF/pdb>). A discussion of the possible value of truncated structures was had as part of the Soak-In at #80 <#80>. <-- any conclusions we can summarise? 6) De Novo Computational Modelling @edwintse <https://github.com/edwintse> @danielgedder <https://github.com/danielgedder> to complete synthesis/procurement of molecules suggested in #85 <#85>. @LauraDS1 <https://github.com/LauraDS1> to book an SPR screen in the last week in August (week of 29th?). @Yuhang-CADD <https://github.com/Yuhang-CADD> to report on progress towards @jhjensen2 <https://github.com/jhjensen2>'s originally-suggested compounds (last update was here <#75 (comment)>) 7) Other Potential Starting Points @chrisdowson1 <https://github.com/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 <https://github.com/mattodd> to clarify that all parties are happy for the data to be released into the public domain. @mattodd <https://github.com/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 <https://github.com/chrisdowson1> to report on progress towards securing the Merck Open Global Health Library <https://www.merckgroup.com/en/research/open-innovation/biopharma-open-innovation-portal/open-global-health-library.html>. 8) Misc/AOB @mattodd <https://github.com/mattodd> to post GRC conference slides somewhere (28 MB...). We need a volunteer to reach out to CC4CARB <https://www.cc4carb-collection.org/> to assess whether we are suitable for a proposal. 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. @Rebecca-Steventon <https://github.com/Rebecca-Steventon> - dose-response data for potential dual inhibitors OSA742, OSA754, OSA759, OSA789 that was summarised in this graphic <#66 (comment)>. 9) Mothballs (if no actions then these need to be linked in wiki and closed) @Rebecca-Steventon <https://github.com/Rebecca-Steventon> has posted data of @LizbeK <https://github.com/LizbeK> fragment screen (https://github.com/opensourceantibiotics/murligase/wiki/Pocket-binding-site <https://github.com/opensourceantibiotics/murligase/wiki/Pocket-binding-site> - but @drc007 <https://github.com/drc007> would like structures to be added). @LauraDS1 <https://github.com/LauraDS1> to liaise with Peter and @LizbeK <https://github.com/LizbeK> to see if a soak of the @eyermanncj <https://github.com/eyermanncj> Enamine compounds is possible at Diamond. Comparative analysis was done by @ZigBu <https://github.com/ZigBu> of mur ligase ATP binding sites (#56 <#56>). Any learnings? @ZigBu <https://github.com/ZigBu> also posted (#57 <#57>) on a paper <https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0152075> highlighting that mur domain movement may not be dependent on substrate binding. Again, anything we need to consider? @eyermanncj <https://github.com/eyermanncj> posted "As a reminder the dynamics of E. coli murD is well established. Here <https://dx.doi.org/10.1038/srep16685> is a “recent” NMR study on E. coli murD." @mattodd <https://github.com/mattodd> @chrisdowson1 <https://github.com/chrisdowson1> have parked the idea of a Euro Lead Factory screen. Do we need to consider the importance of the observed carbamoylation of a residue (Lys198 (-> KCX198) in a structure (7TI7). Does this influence inhibitor design? See @eyermanncj <https://github.com/eyermanncj>'s analysis <#67 (comment)> @eyermanncj <https://github.com/eyermanncj> and @chrisdowson1 <https://github.com/chrisdowson1> to speak to the benefits of ordering the Enamine kinase library. Should this be mothballed? Next Meeting Nov 8th 2pm UK time. The meeting is the Firecracker — Reply to this email directly, view it on GitHub <#90>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABWAURH2QJPWOMIGO5BUTWTWCP7IRANCNFSM6AAAAAARBIVREM>. You are receiving this because you were mentioned.

[mattodd]

Hey @Yuhang-CADD - see above for update from Jan A. Can you please paste a pic below of AZ-13644923 in the same way that you have for the other two AZ compounds above, so that we're clear on the structure and the data we have on it?

[Yuhang-CADD]

Completion of AZ5595 amino derivative:

Still waiting for HRMS
Shipped to Warwick as FA salt

Shipment of compounds:

[Yuhang-CADD]

Sorry Matt I could not find the structure with this numbering, need help from Joe @eyermanncj. I vaguely remember it was from the several compounds we purchased and sent to SSGC, but I could not find the number in the AZ paper...

[eyermanncj]

Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows From: Yuhang ***@***.***> Sent: Tuesday, October 11, 2022 7:32 AM To: ***@***.***> Cc: Eyermann, ***@***.***>; ***@***.***> Subject: Re: [opensourceantibiotics/murligase] Mur Ligase Halloweener Meeting October 2022 (Issue #90) Sorry Matt I could not find the structure with this numbering, need help from Joe @eyermanncj<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Feyermanncj&data=05%7C01%7Cc.eyermann%40northeastern.edu%7Cb344f5c9e8c74630f1a308daab7c4e7a%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C638010847651300726%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=HmbRPeBGdiGCw86k3n4E69eZBTvVB2edKW0iVsnAEww%3D&reserved=0>. I vaguely remember it was from the several compounds we purchased and sent to SSGC, but I could not find the number in the AZ paper<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fpubs.acs.org%2Fdoi%2F10.1021%2Fcb500360c&data=05%7C01%7Cc.eyermann%40northeastern.edu%7Cb344f5c9e8c74630f1a308daab7c4e7a%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C638010847651300726%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=57%2BNQRODQlRSpABNgcgZ0e9beT5WkgHB%2Bzlp2166Xao%3D&reserved=0>... — Reply to this email directly, view it on GitHub<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fopensourceantibiotics%2Fmurligase%2Fissues%2F90%23issuecomment-1274539448&data=05%7C01%7Cc.eyermann%40northeastern.edu%7Cb344f5c9e8c74630f1a308daab7c4e7a%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C638010847651300726%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=fk13L7zN6VRjYxrlKYVDmqh%2FgMYZ0czt%2BNRdqXUg%2FpI%3D&reserved=0>, or unsubscribe<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FARPJVXXKXRJJ2BAIV4OYST3WCVF5RANCNFSM6AAAAAARBIVREM&data=05%7C01%7Cc.eyermann%40northeastern.edu%7Cb344f5c9e8c74630f1a308daab7c4e7a%7Ca8eec281aaa34daeac9b9a398b9215e7%7C0%7C0%7C638010847651300726%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=iLqDvnH8s5SriMFFmq3XhADcVXs0qBdo2ohm6VOf17E%3D&reserved=0>. You are receiving this because you were mentioned.Message ID: ***@***.***>

[danielgedder]

Progress of the synthesis/procurement of molecules suggested in #85<#85>.

[LauraDS1]

221011_LDS_update.pptx

I attached my presentation