Open-Source Coronavirus Monthly Update Meeting #2: Monday 9th May 2022.

[TomkUCL]

Mat says: Meeting link is https://ucl.zoom.us/j/99880132263 I think?

[H-agha]

Initial analysis for all the 51 fragments that bind to NSP13.Fragment analysis for NSP13-Heba Agha.pptx

[jamesday100]

As we are going to get SPR up and running I suggest doing a through assessment of the tool molecules for this protein so we can find a NSP13 tool molecule/s to validate our assays going forward.

For tool molecules you ideally want:

Reported biochemical IC50, ideally confirmed in multiple assays Solubility data X-ray structure confirming its binding mode Chemical stability assessment, eliminate all tool molecules you suspect of being reactive or containing questionable functional groups Full NMR assignment of the structure when you get this in.

In SPR the KD cut off depends on the system (protein) and compound solubility (you want solubility >IC50), so if possible having a solubility assay (NMR) will help illuminate false binders. That will also we useful data for ITC. In our experience for some targets we have not been able to measure >100 uM by SPR which means for mM fragments we simple might not observed binding by SPR. It is not an ideal technique for measurement of weak binders in this range, but its the best option we have at the moment given the protein constraints.

We also talked about using Ligand observed NMR for detection of fragment binding and using ATP (or fluorinated) as the internal control. Ligand observed NMR experiments are also protein hungry, but it is a sensitive assay for detection of low affinity binders in the mM range. Maybe worth looking into if there is anything we can do here.

[TomkUCL]

Please see a recording of yesterday's meeting via the following link;

https://ucl.zoom.us/rec/share/-47aS7MRfGueUxqkAT5I7SuGNPq5Vr7-nZ8J3tgaC_ZqaMA1fCKJCEFr3ok0Ex-e.rppSEhvFCsReiSE3?startTime=1652112140000 Passcode: =WnXR7=K .

Minutes to follow here shortly...

The Enamine REAL space 40 billion top 100 scoring molecules quote can be found here. The decision on the ordering of commercial fragments will be discussed in the next weekly nsp13 meeting. Copy of Quote_1521790_EUR(5641).xlsx

[H-agha]

Agha, Hebaalla has shared a OneDrive for Business file with you. To view it, click the link below. https://adminliveunc-my.sharepoint.com/personal/hebaa_ad_unc_edu/Documents/Attachments/nsp13-fragments.pse.zip [https://r1.res.office365.com/owa/prem/images/dc-zip_20.png]https://adminliveunc-my.sharepoint.com/personal/hebaa_ad_unc_edu/Documents/Attachments/nsp13-fragments.pse.zip nsp13-fragments.pse.ziphttps://adminliveunc-my.sharepoint.com/personal/hebaa_ad_unc_edu/Documents/Attachments/nsp13-fragments.pse.zip

Hi Tom,

I am not able to upload the Pymol session to the GitHub. I got the below message. So, I am attaching it here, in case you can upload it.

Thanks, Heba

[cid:753e6121-94b6-48d8-b515-daa236c74149]

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From: Tom Knight @.> Sent: Tuesday, May 10, 2022 6:19 AM To: StructuralGenomicsConsortium/CNP4-Nsp13-C-terminus-B @.> Cc: Agha, Hebaalla @.>; Mention @.> Subject: Re: [StructuralGenomicsConsortium/CNP4-Nsp13-C-terminus-B] Open-Source Coronavirus Monthly Update Meeting #2: Monday 9th May 2022. (Issue #20)

@H-aghahttps://github.com/H-agha is it possible to upload the PyMol file with ligands bound from slide 7 to the protein for visualization purposes? I'm assuming this is slide 7 but with the protein removed as a separate object?

— Reply to this email directly, view it on GitHubhttps://github.com/StructuralGenomicsConsortium/CNP4-Nsp13-C-terminus-B/issues/20#issuecomment-1122201272, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AWAZRIWYIFFIILY4E6XOQF3VJIZ3LANCNFSM5VKSNXRA. You are receiving this because you were mentioned.Message ID: @.***>