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Mur Ligase Online Research Meeting July 2022 #86

Open mattodd opened 2 years ago

mattodd commented 2 years ago

Date: July 12th 2022 Time: 2pm UK time (other times)
Place: https://ucl.zoom.us/j/91379419977
Recording: https://youtu.be/EEwsGkOniHU Previous Meeting: #76

Apologies: Decks: Please @opensourceantibiotics/murligase remember that if you share slides/info, to drag and drop those into a comment on this page, below.

Agenda:

1) Elaborated Fragments Inhibiting Two Murs

2) Atomwise Hits

3) Variants of AZ Compounds

4) New Protein Structures

As per update from Jan Abendroth in #80, new structures obtained for MurD + UMA? Others?

Update provided by Jan in meeting. Acet MurD with UMA. Got number of crystal forms, all in apo conformation without UMA. Surprising since had worked previously for Psae. Psae MurC - got one molecule per asymmetric unit. Goal to re-grow for soaking with AZ compounds. Was going to get those re-screened and do soaking (had seen good thermal shifts for).

Mothball this? --> 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, or can this be mothballed?

A discussion of the possible value of truncated structures was had as part of the Soak-In at #80

5) De Novo Computational Modelling

6) Other Potential Starting Points

7) Misc/AOB

8) List of 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

Aug 9th 2pm UK time for those of us not on vacation.

Yuhang-CADD commented 2 years ago

General Progress To Date

Synthesis of Amino AZ5595

WYH21_22_ reaction scheme Amino AZ5595 Verified by HRMS and NMR

Shipment of Compounds

OSA_Compound List

Micro ED Results

OSA_001041 (WYH5-4-P) The structure was resolved image

OSA_001048 (WYH13-4-P) The structure was not resolved due to the lack of suitable crystals (also might be deterioration of the amine, will send new batch to them later on)

OSA_001042 (WYH6-2-P) The structure was attempted and failed due to the presence of multiple lattices and lack of reflections. (Weird, as this structure had been resolved by X-ray crystallography already and was sent as a positive control)

AZ cmpd 4 (OSA_001044, WYH9-2-P)

PDB structure was submitted by Peter last month but not yet shown on the database, I am guessing it has not yet been through the publication process?

De Novo Computational Modelling_Jan's Predictions

Suzuki reaction started for ConfGen17 Testing reported conditions, LCMS showed no product peak. image Potential reasons:

  1. catalyst expired
  2. ring-opening of the substrate 2 and completely transformed into other byproducts (may need to couple the amine substrate 1 with Boc-Glycine first)
  3. conditions reported not suitable for the system.
edwintse commented 2 years ago

These are the four multitargeting inhibitors from Adrian's slides last meeting

Untitled Wiley-2

Yuhang-CADD commented 2 years ago

Alternative/additional strategies for improving accumulation

picture Incorporating the structural features of known Efflux Pump Inhibitors (EPI) into the amine product?

mattodd commented 2 years ago

Jan/Peter have submitted the structure of @Yuhang-CADD compound (OSA_001044) bound to Pae MurC: Title : Pseudomonas aeruginosa MurC with WYH9-2-P - OSA_001044 Corresponding authors : Peter Horanyi, Jan Abendroth, Wang Yuhang, Matthew Todd, Isabelle Phan, Peter Myler, Donald Lorimer, Tom Edwards Your deposition D_1000267042 is assigned the following accession code(s): PDB ID 8DOF Thanks Jan.

mattodd commented 2 years ago

@Yuhang-CADD I'm listening to a talk by Helen Zgurskaya Described here I think: https://journals.asm.org/doi/10.1128/mBio.02785-20 Take a look and see if there are some design criteria we can use?

Yuhang-CADD commented 2 years ago

Hi Matt,

Thanks for sharing this wonderful paper!

According to the paper, the rules may vary as the bacterial species-specific differences in the composition of the OM and efflux pump plays a role.

Such as the eNTRy way rules only applies to E.Coli and other enterobacteria due to the permeability properties of general porins dominate the OM and eject molecules based on their size, shape and electrostatic properties.

In P.ae, substrate specificities of the transporters (of efflux pumps) and efflux constant are the major drivers of efflux avoidance rules. The paper claimed a developed and validated model that describes the avoidance and inhibition of active efflux in P.ae.

From my shallow understanding of this paper, I think our focus should be on the rules/features for efflux avoidance instead of inhibition considering the way our hits (such as AZ5595 amine derivative) were expected to behave.

Thus, as the paper listed (also useful/applicable in our system), an increase in the number of hydrogen bond acceptors (HBAs) is correlated with strong efflux avoidance (our hits like AZ5595 or its amine derivative do have more than 5 N or O atoms within the structure). Also, a reduced acylindricity and anisotropic polarizability of the substrate's structure may also help reduce the efflux effects towards it (our compounds also have this feature, so no worries for now I assume).

In summary, based on the structural information of our compounds (AZ derivatives), I think they do match the criteria we extracted from the paper (mentioned above).

But please let me know if my perspective needs to be corrected.

Many thanks! Yuhang

mattodd commented 2 years ago

Laura and Adrian Slides.

Slide 1, from Laura:

Screenshot 2022-07-12 at 14 05 30

There was discussion of what the best concentration of compounds might be - micromolar to millimolar. Also soaking vs co-cryst; e.g. UMA system without ADP with/without Mg2+ (some discussion of optimal Mg2+ conc at 11 mins), with relatively high concentration of test compound. Crystal samples (EcMurD:UMA, and Apo EcMurE and apo EcMurD both in the presence of all four Enamine compounds) have been sent to Diamond.

Slide 2, from Adrian (starts 12:55 ends 16:35)

Screenshot 2022-07-12 at 14 16 22

Enamine library Pae MurE hit N15. Data possible suggesting N15 binds in a way that incompletely occludes MurE active site. Two undergrads are starting at Warwick to pursue Enamine hits (they can be invited to the meetings...) - let's connect them up to everyone else.