Open mattodd opened 2 years ago
Amino AZ5595 Verified by HRMS and NMR
OSA_001041 (WYH5-4-P) The structure was resolved
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)
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?
Suzuki reaction started for ConfGen17 Testing reported conditions, LCMS showed no product peak. Potential reasons:
These are the four multitargeting inhibitors from Adrian's slides last meeting
Incorporating the structural features of known Efflux Pump Inhibitors (EPI) into the amine product?
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.
@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?
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
Laura and Adrian Slides.
Slide 1, from Laura:
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)
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.
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
[ ] @AJLloyd105 @chrisdowson1 @LauraDS1 to update on further screening of the Warwick Enamine Collection. In meeting update was provided. Screenshots shown below. @chrisdowson1 mentioned in meeting that a new data analysis method has come online that will help with determination of Km etc, which should speed things up. Millimolar concentrations had been used, starting at 2 mM then diluting. Some compounds were down in the 20-100 uM inhibitors so @eyermanncj suggested trying lower concs. @chrisdowson1 suggested trying co-cryst rather than just soaking (since structural change is happening). Competitive swap out with the ADP experiments had been tried. @eyermanncj suggested UMA without ADP was the best one to go for. Exchange needs a high conc of compound, which @LauraDS1 is doing, and the presence of magnesium ions. @eyermanncj asked whether the Mg2+ is getting in the way? @AJLloyd105: there is a known optimum for Mg2+ conc. If too high may start to generate interfering chelates. @AJLloyd105 reported that compound N15 (see slides) appeared to be occluding, not completely inhibiting. Warwick project students are pursuing the next hits. (Can we get them on Github so that they can work with us on design?)
[ ] @eyermanncj @LauraDS1 to update on any additional compounds that have consequently been ordered/evaluated
[ ] @LauraDS1 to update on screening (inhibition, SPR, soak) of elaborated fragments sent by @edwintse in #84 Enzymatic evaluation scheduled.
[ ] @LauraDS1 @LizbeK to update on any further fragment soaking and/or co-crystallisation experiments. Comments in meeting: MurD and MurE from E coli had been used in crystallisation experiments with no ligands bound: giving open structures. Hit rate with small molecules is low. To improve: co-cryst with other ligands, then soak. e.g. MurD with ADP, ADCDP, UMA. Jan Abendroth also got structure of Psae and Ace MurD with UMA. Working on further structures (below). Laura has already ordered some compounds from the assays, and those have arrived, so plates are being set up for structural work. Psae MurC (being purified this week), D and E. @edwintse will ship 14 elaborated fragments to Warwick.
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.