Fragment hit to lead - Round 1&2: crystallography

[KatoLeonard]

Dear @LizbeK @LauraDS1, As you might know, I am planning a short research stay at Oxford University to gain insight into the biologic part of the project. This would be the perfect time to obtain crystal structures of a mur ligase with Dana's compounds (6) that showed dual target inhibition for murD and murE. My question is if you have enough of Dana's samples to do the X-ray screen, if not I can bring more of them with me. How much of the compounds would be needed then? My second questions concerns the compounds I designed and synthesised, which you can see below. How much of my compounds (solids) should I bring to Oxford to obtain crystal structures with a mur ligase? ?

[LauraDS1]

Hi Kato,

I have already done soaking of EcMurE and EcMurD and those dual compounds plus the AZ compound. I'm looking into something I found from these experiments. To make the story short, no hits were found. I already set up co-crystallisation experiments with those compounds as well. Maybe it can be discussed after tomorrow's meeting in case new data is shown and we have other compounds worth trying. The EcMurD are still not super reproducible. You could give that a try as well. Anyway, I think we should set up a meeting and discuss everything so we don't end up running the same experiments.

[mattodd]

Interesting. We can talk in the meeting tomorrow (#66) but @LauraDS1 you'd expect the AZ compound to be in there, right? Isn't that a positive control? Doesn't it inhibit MurD? @Yuhang-CADD @eyermanncj ?

[eyermanncj]

We have no MurD data for the AZ compounds. Waiting for Warwick to test. They have received the AZ compounds now so hopefully MurD IC50 data for the AZ compounds in the near future. @mattodd @LauraDS1 @Yuhang-CADD @chrisdowson1 @Rebecca-Steventon

[LauraDS1]

@mattodd The EcMurE crystals show a more close conformation with the AZ compound and the dual inhibitors. I also tried ADP soaks which completely melted both EcMurE and EcMurD crystals, as expecting. If the compounds are inducing a similar conformational change to the ADP binding, that could explain the conformational change of EcMurE crystals and why I couldn't see anything bound (the ligand bound form would no longer be part of the crystal).

Adrian should be showing AZ compound data tomorrow.

Just an additional note: we have done all soaks and assays with the compound WYH9-2-P Yuhang sent us.

[eyermanncj]

@LauraDS1 @mattodd

Interesting results for ADP and EcMurD as there is a EcoMurD ADP structure in the PDB 2UAG

https://www.rcsb.org/experimental/2UAG

https://www.sciencedirect.com/science/article/pii/S0022283699928000?via%3Dihub EcoMurD ADP JMB 1999.pdf

Are you including UMA in your crystal systems?

[LauraDS1]

They had a different system. I'm not including UMA on my crystals. @eyermanncj

[mattodd]

@KatoLeonard for the compounds above (KL2-9) can you please just confirm that they are in the master list with suitable OSA numbers? Here's the convention again. And could @KatoLeonard and @edwintse please post the current synthesis target list for elaborated fragments that we're pursuing in the lab, following @Rebecca-Steventon 's data on the effectiveness of OSA759.

[edwintse]

@mattodd Here is the list of potential synthetic targets from Kato. I've listed the prices of the bromides or boronates based on the cheapest option. All cLogP values are based off Chemdraw. I also added 3 extra suggestions on the RHS that may be possible. Let me know your thoughts and I can make the purchase of the compounds.

[mattodd]

Hi @edwintse - great, thank you. I think we should get the lot. Please go ahead and order.

[KatoLeonard]

Hi @mattodd, KL2-9 all set up in the Master spread sheet as OSA_001054 - OSA_001061. And here are the documents with my proposals for the new fragments. New Compounds Quotes.xlsx