drc007
commented
3 years ago Hi,
I probably won’t make the meeting. Having house electrics overhauled so no power for most of the day.
Re https://github.com/opensourceantibiotics/murligase/wiki/Allosteric-Pocket https://github.com/opensourceantibiotics/murligase/wiki/Allosteric-Pocket Could we add the structures to the web page please :-)
Regarding the docking studies vs MurC, lots of interest when I posted on Twitter. David Koes would also like to run a docking study and others have expressed an interest (but not enough to comment on GitHub). I wonder if we should publicise this a bit more?
Cheers,
Chris
On 5 Jul 2021, at 22:40, Mat Todd @.***> wrote:
Meeting follows on from June 2021 meeting at #44 https://github.com/opensourceantibiotics/murligase/issues/44. When: Tue July 6th 2pm London (BST). Where: https://ucl.zoom.us/j/91614633419 https://ucl.zoom.us/j/91614633419 Recording:
Actions from Last Time
@WieselHenson to complete the synthesis of the AZ alcohol compound @Rebecca-Steventon https://github.com/Rebecca-Steventon to post data of @LizbeK https://github.com/LizbeK fragment screen (Done: https://github.com/opensourceantibiotics/murligase/wiki/Allosteric-Pocket https://github.com/opensourceantibiotics/murligase/wiki/Allosteric-Pocket) and perform screen of @danaklug https://github.com/danaklug elaborated fragments. Laura to continue crystallisation trials of MurD and MurE in Warwick, with the plan to take crystals to Diamond @eyermanncj https://github.com/eyermanncj, Chris and @bartrum https://github.com/bartrum to pursue AZ compound shipment for crystallisation trials. @jhjensen2 https://github.com/jhjensen2 to extract in vitro inhibition data from published literature and use towards the construction of a predictive model. Peter Horanyi to continue crystallisation of e.g. MurC with Enamine compounds sent by @eyermanncj https://github.com/eyermanncj. (Structures here https://github.com/opensourceantibiotics/murligase/issues/42#issuecomment-822081038 from @loriferrins https://github.com/loriferrins) Chris Dowson to liaise with others to establish protein needs, and what's needed from SSGCID. @mattodd https://github.com/mattodd and Chris D to interact with Alphafold. With Laura they'll come up with a defined piece of work and circulate. @bartrum https://github.com/bartrum to liaise with David Baker lab about potential protein structure prediction work. Laura to liaise with Peter and Lizbe to see if a soak of the @eyermanncj https://github.com/eyermanncj Enamine compounds is possible at Diamond. Following some discussion at May meeting, @eyermanncj https://github.com/eyermanncj asked whether there might be the possibility of a biochemical screen against another non-ATP site, and Chris D would chat to Adrian about that. June meeting posted to Youtube: Additional items for discussion:
New docking studies vs MurC described in #46 https://github.com/opensourceantibiotics/murligase/issues/46 discussed by @jhjensen2 https://github.com/jhjensen2 @drc007 https://github.com/drc007 @dkoes https://github.com/dkoes and @cstein https://github.com/cstein @Rebecca-Steventon https://github.com/Rebecca-Steventon's data on Dana's elaborated fragments. Biochemical hits found? How to gain structural insights? Time to bring in modelling team? Atomwise shipment Status of ELF Screen application Overall Aims remain: i) Structures of two mur ligases bound to the same small molecule. ii) Identify new starting points for inhibitors.
Future logistical aim: devise platform legal agreements within OSA in order to simplify the MTA-related paperwork, which is proving problematic. (Could we transform OSA into a charity (though since none of us would work for this charity, it's not clear how much that might help)).
Next meeting: Tuesday 3rd or 10th August 2pm BST London Location:
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jhjensen2
mattodd
Yuhang-CADD
chrisdowson1
Meeting follows on from June 2021 meeting at #44. When: Tue July 6th 2pm London (BST). Where: https://ucl.zoom.us/j/91614633419 Recording: https://youtu.be/lAWCUQGDGtY
Actions from Last Time
Additional items for discussion:
New docking studies vs MurC described in #46 discussed by @jhjensen2 @drc007 @dkoes and @cstein. The approach aims to find new molecules that are predicted to bind better than commercially-available molecules (which are predicted first, as a baseline <-- indicating what scores to beat). The structures shown in the meeting are commercial. The genetic algorithm (which is expected to find things that are not commercially available) was running at the time of the meeting. Relatively simple things to predict (on an input set size of ca. 400k compounds) like logP (and even synthetic accessibility) can be included in the algorithm. @chrisdowson1 was hoping for the application of an Entryway filter, to aim for compounds that might accumulate intracellularly. Question was whether the Entryway web tool could easily deal with batches - we're not 100% sure. Could in theory do a post- or pre-screen. Hergenrother could provide code, to allow us to implement? Action on @mattodd to loop in Jan and Paul H to see what can be done. Aside from the genetic algorithm, the existing predictions show predicted strong binders from Zinc. How do we source these Zinc compounds? They are not necessarily "in stock": MolPort suggests only two of them are in stock, though the ones suggested do not look difficult to make. (note in this case the search was done with a smaller set of molecules from Enamine vs a larger set from Zinc). Could use a larger set (250k) from Enamine; advantage being all purchasable. The genetic algorithm compounds will need to be made, and at that point we'd likely benefit from an automated retrosynthesis algorithm that Jan can implement.). Jan is hoping for experimental validation of the genetic algorithm approach (to show it's worth doing). Follow-up Q1: It would be useful if we could generate the pictures of the poses of the best predicted binders, to learn about what may be productive places to bind to the enzyme. @cstein may have these. Follow-up Q2: Could we re-dock the e.g. top 100 hits vs another mur ligase, as part of the multi-targeting approach (or even against the same enzyme in another species...)? @jhjensen2 said yes, and even better might be to have the genetic algorithm optimise simultaneously vs two Mur targets. Caveat from Jan: this is docking ("guessing with style", said Chris). Peter Horanyi asked whether we could screen out compounds that are similar to others, thereby increasing diversity; Jan said yes via calculating a similarity score (and eliminating any with low scores that are similar to ones with high scores), though Jan does not want to triage compounds before the medchemist sees them (i.e. maybe we just need clustering of similar structures in a tree). Machine learning can be done too, which can kick in better when we have ca 50 experimental data points; for validation of the docking we'd need fewer datapoints. For visualization of the compounds in this project we can all use Datawarrior to display structures and cluster by similarity? (sdf files are useful for this). @Yuhang-CADD asked how many samples we can test biologically, to validate the approach. This is a resources question... Yuhang also asked whether we could score these suggestions with other software; Jan said yes, this is possible, but you need expertise in those platforms; SMILES are available, so anyone can have a go at such consensus modelling and provide inputs (i.e. need people to drive those comparisons).
Possible publicising of the challenge..?
@Rebecca-Steventon's data on Lizbe's fragments. Where are the structures? Action on @LizbeK to dig those up and put somewhere. Also new data from Becca on Dana's elaborated fragments. Biochemical hits found at 1 mM. 78 compounds tested. 11 compounds gave >80% inhibition vs 2.5 ug/mL Streptococcus agalactiae(?) MurD, and those were run against Streptococcus agalactiae MurE with some inhibiting both (i.e. dual inhibition!). Most compounds inactive (i.e. not the case that, at those high concentrations, everything is active) and some compounds hit one enzyme better than the other.
How to gain structural insights, i.e. motifs in the actives that are not in the inactives, etc? @chrisdowson1 suggested sending the actives to Jan to verify predicted binding? Useful, but fragments are even more difficult to predict. Co-crystal formation desirable if the hits confirmed - at the moment Laura was hoping for a better crystal system for MurD. Currently Streptococcus agalactiae MurD and E. coli MurE.
@eyermanncj suggested that we need full 10-point dose response curves to be sure of the inhibition observed. Dual inhibitors are the priority. @Rebecca-Steventon said this was doable if targeting the small number of compounds exhibiting dual inhibition (not all 78) (Action on Becca). The assay is functional, though the predicted binding site is allosteric (not ATP-competitive) (need to point to where (on the wiki) these are binding). Question: how's the conservation of the site out in the allosteric position across ESKAPE/other pathogens? Status of MurC (pseudomonas) screen in Warwick?
Shipment of Yuhang's AZ compound will take place as soon as the identity is confirmed by NMR. e.g. to Bart first. Peter has Acetobacter and Psuedomonas MurC.
Atomwise shipment - nearing the end of the legal quest, hopefully.
Status of ELF Screen application?
Note that experimental screening is done in the presence of metal ions (e.g. Mg2+); crystallography - can't tell what is a water and what is a magnesium ion; computational docking removes waters and metal ions on the assumption that small molecules would displace those.
Overall Aims remain: i) Structures of two mur ligases bound to the same small molecule. ii) Identify new starting points for inhibitors.
Future logistical aim: devise platform legal agreements within OSA in order to simplify the MTA-related paperwork, which is proving problematic. (Could we transform OSA into a charity (though since none of us would work for this charity, it's not clear how much that might help)).
Next meeting: Tuesday 3rd August 2pm BST London Location: https://ucl.zoom.us/j/98754959307