Mur Ligase Meeting September 2024

[Yuhang-CADD]

Date: Sep 10th 2024
Time: 2pm UK time other timezones

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

Recording:

Previous Meeting: #112
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 (including MICs, retests of IC50s at a lower concentration). Also, any updates on AZ compounds vs TB? @LauraDS1

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 Compound to Warwick Inhibition Assay Jun 2022 #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) need complete data.
• @Yuhang-CADD's 4th batch of fresh samples of AZ5595 and derivatives (Rigid Small Amines & Guanidiniums & Pyridiniums) in progress.
• Accumulation assay - @mattodd to reach out possible collaborators @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

Oct 8th 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.

[mattodd]

Nice new review from Laura Piddock et al.
https://www.nature.com/articles/s41591-024-03218-w

[Yuhang-CADD]

GBD 2021 Antimicrobial Resistance Collaborators on analysis of global AMR burden (1990-2021) with forecasts to 2050

https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(24)01867-1/fulltext

Brief Summary:
The growing threat of AMR (especially among old people_50s and older, 70s worse) is threatening with drastic growth in MRSA mortality and GNB resistance to carbapenems. More AMR caused deaths are estimated (1.91M) by 2050.
Regional and age differences matter.
Call for global interventions on this issue with coordinated policies and investment in this field for better ABX development and infection control (reducing overuse of ABXs in agriculture and healthcare as was highlighted in O'Neil's systematic review back in 2016).

[Yuhang-CADD]

Nice new review from Laura Piddock et al.
https://www.nature.com/articles/s41591-024-03218-w

Advancing global antibiotic research, development and access

Brief Summary:
Pipeline of ABX development inadequate
Lack of innovation and investment in new drug classes (also see this D Klug, M Todd et al)
Companies and researchers withdrawing from the market/field (brain/moneydrain in ABX research).
Push (CARB-X, NIH, etc) and Pull (UK subscription Model, US GAIN Act, etc) Incentives not working: high costs & low financial returns, support insufficient for ABX developmental circle (early-stage R&D no followups) and meet global scaled needs (no coordinated international actions)
Global inequities in ABX access (income wise)[GARDP is working hard on making new ABX available in low-middle income regions]

[Yuhang-CADD]

Complete Chemical Scheme

Yellow: on the make
Green: synthesized
Red: failed on synthesis
About the Pyridiniums: deteriorate upon vac-down, will have plenty of water after purification, will try Cyrotrap method (one last try) or abandon (considering their lowest tendency to be a good accumulator)

[Yuhang-CADD]

Analysis and Hypothesis

Due to the lack of AZ compounds in full length MurC, the interactions between one side chain of AZ scaffolds and the protein (truncated central domain) were missing. [Looking forward to Laura and Scott's Xstals!) which made the side chain modifications of AZ derivatives more difficult to predict.

Hypothesis on the side-chain interaction map:
Note: the pyrazolopyrimidine core and pyrazole side chain have been proven to bind to the MurC consistently the way described, details see (PDB: 6X9F, 6X9N, 8DOF)
Side-chain is represented by "G" and the linking group is represented by "Y".
In different structures, the size of G can vary, shortest within the proposed hydrophobic area, longest reaching the proposed hydrophilic area.

Structural validation:

AZ alcohols with nanomolar potency (functional groups to fit into the hydrophobic pocket on the G site and the extending alcohol to fit the hydrophobic pocket/just maintaining hydrophilic interactions)

AZ derivatives with micromolar potency (either due to extra charge that caused the compound harder to enter/pose in MurC the way AZ alcohols do, or lack of hydrophilic interactions from the extended end)

AZ rigid derivatives with bad potency [hydrophilic amine in the hydrophobic pocket or just completely does not fit in (TR1-4-BP)]

Furthermore, checking the original Hameed paper, all of the potent ones have such hydrophobic contacting group on the side chain and then extending to have a polar hydrophilic ending.

Final validation sets:

Especially

1. TR6-4-P and TR6-8-P as decent length of the extended polar end to reach the hydrophilic interaction area while bearing no lipophilic interactions within the linker -CH2CH2-
2. WYH32-P super extended polar end as a prolonged polar control with no nonpolar interactions in the linker (more of a repellation as the linkers contains multiple oxygen, polar), see if the end of it extends outside the polar area, and altogether gives a even worse IC50.

[Yuhang-CADD]

Warwick's contribution to the IC50s and Ki of 3rd_round_shipments_AZ_chapter2_Yuhang Aug 2024-2.pptx

[Yuhang-CADD]

Nice new review from Laura Piddock et al.
https://www.nature.com/articles/s41591-024-03218-w

Advancing global antibiotic research, development and access

Brief Summary: Pipeline of ABX development inadequate Lack of innovation and investment in new drug classes (also see this D Klug, M Todd et al) Companies and researchers withdrawing from the market/field (brain/moneydrain in ABX research). Push (CARB-X, NIH, etc) and Pull (UK subscription Model, US GAIN Act, etc) Incentives not working: high costs & low financial returns, support insufficient for ABX developmental circle (early-stage R&D no followups) and meet global scaled needs (no coordinated international actions) Global inequities in ABX access (income wise)[GARDP is working hard on making new ABX available in low-middle income regions]

Additional Perspectives:

Achieving sustainable access to antibiotics is more than just a last mile challenge
https://www.nature.com/articles/s41579-024-01083-5

The AMR Accelerator: from individual organizations to efficient antibiotic development partnerships

https://www.nature.com/articles/d41573-024-00138-9