StructuralGenomicsConsortium / CNP4-Nsp13-C-terminus-B

An SGC Open Chemical Networks Project Devoted to a site on the SARS-CoV-2 protein nsp13
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Open-Source Coronavirus Monthly Update Meeting #6: 17:00-18:00 BST, Monday 14th November 2022 #30

Open TomkUCL opened 1 year ago

TomkUCL commented 1 year ago

Date: Mon Nov 14th 2022 Time: 5pm UK time (other times)
Place: https://ucl.zoom.us/j/97172937586 Recording: Apologies - forgot to record this one... Previous Meeting: issue #29
Who can come?: Anyone. No need to say anything unless you'd like to. If you'd like to contribute, please join Github.

Attending: @mattodd @TomkUCL @SumeraMalik123 @toluene44 @ahsgc @tmw20653 @jamesday100 @kipUNC

Apologies: none

Decks: Please @StructuralGenomicsConsortium/cnp4-nsp13 remember that if you share slides/info, to drag and drop those into a comment on this page, below. Very easy and saves @mattodd having to pester you.

@StructuralGenomicsConsortium/cnp4-nsp13 rough agenda, sorry for lateness:

Agenda:

1) Status and planning for the SPR assay #25

@TomkUCL to update. In meeting: Traces obtained for control compound ("PUG") look similar to those in lit, though issue of using correct buffers needs to be sorted out. Next runs: can try the non-hydrolyzable analog of ATP, then the Enamine test compounds. @SumeraMalik123 updated that she had completed her S{R screen of these compounds and found about 3 hits. Compounds also screened vs MERS Nsp13. Compounds had been screened in ATPase assay, with some activity. @ahsgc to summarise these hits (data on Signals) and provide thoughts on SAR, since we can order compounds possessing similar structures.

It would be useful to try these compounds on the Creoptix Wave.

2) Molecule Procurement.

Where we are up to with the set of molecules predicted by Kostya to be binders - the comparison between the Enamine docking set and the generative set. Including updates on chemistry from Tom and Anwar (pyramal) - what's already come in, what's coming in, what's scheduled and whether any molecules are currently not scheduled for delivery (and might need replacing). In meeting:

3) Which compounds should be sent to Joe Newman at Oxford/Diamond for a crystal soak?

Offer of a crystal soak from Joe Newman. Which compounds to send? In meeting: Certainly the compounds identified in 1) above. Also any other hits found by @TomkUCL in SPR screen. Plus any other compounds identified before cut off in 1-2 weeks time. Maybe PUG compound? Amount needed: If in DMSO at e.g. 50-100 mM then liquids preferred to save time with dissolving (10 ul is enough), otherwise around 1-5 mg of solid is more than enough. Will do 20 at a time.

(Hopefully we can simply send from UCL and not have to reorder compounds).

4) What's needed next in the helicase review?

5) AOB

@jamesday100 is thanked for his ongoing role as Pharma Champion for this project.

Next Meeting Dec 12th 5pm UK time at https://ucl.zoom.us/j/97172937586

L'esprit de l'escalier If you'd like to follow up after the meeting, please comment below. You can also email, but please be clear if anything in the email should not be public domain - the default is open.

Evert-Homan commented 1 year ago

Hi Tom,

Thanks for the invite but I need to refrain, I have too many projects on my plate as it is.

BW/Evert

From: Tom Knight @.> Sent: Tuesday, 15 November 2022 12:16 To: StructuralGenomicsConsortium/CNP4-Nsp13-C-terminus-B @.> Cc: Evert Homan @.>; Team mention @.> Subject: [StructuralGenomicsConsortium/CNP4-Nsp13-C-terminus-B] Open-Source Coronavirus Monthly Update Meeting #6: 17:00-18:00 BST, Monday 14th November 2022 (Issue #30)

Date: Mon Nov 14th 2022 Time: 5pm UK time (other timeshttps://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.timeanddate.com%2Fworldclock%2Fmeetingdetails.html%3Fyear%3D2022%26month%3D11%26day%3D14%26hour%3D17%26min%3D0%26sec%3D0%26p1%3D43%26p2%3D136%26p3%3D37%26p4%3D771%26p5%3D235%26p6%3D152%26p7%3D770%26p8%3D250%26p9%3D196%26p10%3D240&data=05%7C01%7Cevert.homan%40ki.se%7C1c492cd74d5b428cbc4c08dac6fad591%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C638041077877123141%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=NUIkAchUF3YVQhbzkIbiM1Tdwao%2FSUOG8lrGrSqntts%3D&reserved=0) Place: https://ucl.zoom.us/j/97172937586https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fucl.zoom.us%2Fj%2F97172937586&data=05%7C01%7Cevert.homan%40ki.se%7C1c492cd74d5b428cbc4c08dac6fad591%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C638041077877123141%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=4GjpaHvTEytYJr%2Fn4t4pQDeCwuqTQR45ag9b5LLjDJI%3D&reserved=0 Recording: Apologies - forgot to record this one... Previous Meeting: issue #29https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FStructuralGenomicsConsortium%2FCNP4-Nsp13-C-terminus-B%2Fissues%2F29&data=05%7C01%7Cevert.homan%40ki.se%7C1c492cd74d5b428cbc4c08dac6fad591%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C638041077877123141%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=R430fZtJolUZaAm5j6N%2BEnYulzdCAZYDMMGsWMRSjkc%3D&reserved=0 Who can come?: Anyone. No need to say anything unless you'd like to. If you'd like to contribute, please join Github.

Attending: @mattoddhttps://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fmattodd&data=05%7C01%7Cevert.homan%40ki.se%7C1c492cd74d5b428cbc4c08dac6fad591%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C638041077877123141%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=LZ6wm5PXlilteOkLh4QHH0rZCf2sFFXUUWIZu2Ls0KA%3D&reserved=0 @TomkUCLhttps://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FTomkUCL&data=05%7C01%7Cevert.homan%40ki.se%7C1c492cd74d5b428cbc4c08dac6fad591%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C638041077877123141%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=CzSWZvn1qrclhPCFOmFJTED%2Bvw43vjW9IHEar7vKKtg%3D&reserved=0 @SumeraMalik123https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FSumeraMalik123&data=05%7C01%7Cevert.homan%40ki.se%7C1c492cd74d5b428cbc4c08dac6fad591%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C638041077877123141%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=18EKAXLR7RtKs3GH4nH9HC6HRhm%2Bugch%2BjoutKdIQss%3D&reserved=0 @toluene44https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Ftoluene44&data=05%7C01%7Cevert.homan%40ki.se%7C1c492cd74d5b428cbc4c08dac6fad591%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C638041077877123141%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=AJurVzbDmVbSi5jXI2twJTqyN5hqmalNwpV9xYs1o6E%3D&reserved=0 @ahsgchttps://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fahsgc&data=05%7C01%7Cevert.homan%40ki.se%7C1c492cd74d5b428cbc4c08dac6fad591%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C638041077877123141%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=bjN8DUnJdZOhrtr4T2QHhv1fdpXjfvoqkmryqavb1kg%3D&reserved=0 @tmw20653https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Ftmw20653&data=05%7C01%7Cevert.homan%40ki.se%7C1c492cd74d5b428cbc4c08dac6fad591%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C638041077877123141%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=qImzZxgGYv1GHNSe9fPMM5tOmWoEUZfU0ebkE8cgde8%3D&reserved=0 @jamesday100https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fjamesday100&data=05%7C01%7Cevert.homan%40ki.se%7C1c492cd74d5b428cbc4c08dac6fad591%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C638041077877123141%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=8M7c%2BDthDHH8lyEr0xFktDLw4f89bur7YLNY8mDPNfg%3D&reserved=0 @kipUNChttps://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FkipUNC&data=05%7C01%7Cevert.homan%40ki.se%7C1c492cd74d5b428cbc4c08dac6fad591%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C638041077877123141%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=SM86mMGci3Si3KGtKYWsAby5VpoLCJH%2BgY5v4g%2B8%2B64%3D&reserved=0

Apologies: none

Decks: Please @StructuralGenomicsConsortium/cnp6-abhd2https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Forgs%2FStructuralGenomicsConsortium%2Fteams%2Fcnp6-abhd2&data=05%7C01%7Cevert.homan%40ki.se%7C1c492cd74d5b428cbc4c08dac6fad591%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C638041077877123141%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=GJC0RD6p9xo828PpnzePN9yU3gCKcwlC8XjvSAkUiM4%3D&reserved=0 remember that if you share slides/info, to drag and drop those into a comment on this page, below. Very easy and saves @mattoddhttps://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fmattodd&data=05%7C01%7Cevert.homan%40ki.se%7C1c492cd74d5b428cbc4c08dac6fad591%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C638041077877123141%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=LZ6wm5PXlilteOkLh4QHH0rZCf2sFFXUUWIZu2Ls0KA%3D&reserved=0 having to pester you.

@StructuralGenomicsConsortium/cnp4-nsp13https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Forgs%2FStructuralGenomicsConsortium%2Fteams%2Fcnp4-nsp13&data=05%7C01%7Cevert.homan%40ki.se%7C1c492cd74d5b428cbc4c08dac6fad591%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C638041077877123141%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=vWYztTeI4Jzgs1qfEkhFPwqlAZAOdX4ZjXXC6LgCXEw%3D&reserved=0 rough agenda, sorry for lateness:

Agenda: 1) Status and planning for the SPR assay #25https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FStructuralGenomicsConsortium%2FCNP4-Nsp13-C-terminus-B%2Fissues%2F25&data=05%7C01%7Cevert.homan%40ki.se%7C1c492cd74d5b428cbc4c08dac6fad591%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C638041077877123141%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=oYkbJOYO9KVyvQcLmXqP1EYSj2llL%2Fljj0%2FxaTawD8o%3D&reserved=0

@TomkUCLhttps://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FTomkUCL&data=05%7C01%7Cevert.homan%40ki.se%7C1c492cd74d5b428cbc4c08dac6fad591%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C638041077877123141%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=CzSWZvn1qrclhPCFOmFJTED%2Bvw43vjW9IHEar7vKKtg%3D&reserved=0 to update. In meeting: Traces obtained for control compound ("PUG") look similar to those in lit, though issue of using correct buffers needs to be sorted out. Next runs: can try the non-hydrolyzable analog of ATP, then the Enamine test compounds. @SumeraMalik123https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FSumeraMalik123&data=05%7C01%7Cevert.homan%40ki.se%7C1c492cd74d5b428cbc4c08dac6fad591%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C638041077877123141%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=18EKAXLR7RtKs3GH4nH9HC6HRhm%2Bugch%2BjoutKdIQss%3D&reserved=0 updated that she had completed her S{R screen of these compounds and found about 3 hits. Compounds also screened vs MERS Nsp13. Compounds had been screened in ATPase assay, with some activity. @ahsgchttps://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fahsgc&data=05%7C01%7Cevert.homan%40ki.se%7C1c492cd74d5b428cbc4c08dac6fad591%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C638041077877279344%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=7T194I5NBzgJyAcA%2Bra3VZQGm1OJypoh7DYzPYCjutc%3D&reserved=0 to summarise these hits (data on Signals) and provide thoughts on SAR, since we can order compounds possessing similar structures.

It would be useful to try these compounds on the Creoptix Wave.

2) Molecule Procurement.

Where we are up to with the set of molecules predicted by Kostya to be binders - the comparison between the Enamine docking set and the generative set. Including updates on chemistry from Tom and Anwar (pyramal) - what's already come in, what's coming in, what's scheduled and whether any molecules are currently not scheduled for delivery (and might need replacing).

3) Which compounds should be sent to Joe Newman at Oxford/Diamond for a crystal soak?

Offer of a crystal soak from Joe Newman. Which compounds to send? In meeting: Certainly the compounds identified in 1) above. Also any other hits found by @TomkUCLhttps://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FTomkUCL&data=05%7C01%7Cevert.homan%40ki.se%7C1c492cd74d5b428cbc4c08dac6fad591%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C638041077877279344%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=1KbqRDoVLWM2chx1B2vLN3kW%2Bhzq%2BOt7nMoegwM0css%3D&reserved=0 in SPR screen. Plus any other compounds identified before cut off in 1-2 weeks time. Maybe PUG compound? Amount needed: If in DMSO at e.g. 50-100 mM then liquids preferred to save time with dissolving (10 ul is enough), otherwise around 1-5 mg of solid is more than enough. Will do 20 at a time.

(Hopefully we can simply send from UCL and not have to reorder compounds).

4) What's needed next in the helicase review?

5) AOB

@jamesday100https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fjamesday100&data=05%7C01%7Cevert.homan%40ki.se%7C1c492cd74d5b428cbc4c08dac6fad591%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C638041077877279344%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=uq9mkN6bGp5dodv5kVt%2BqeKv%2FAoO8JWBBaz36mPmpjI%3D&reserved=0 is thanked for his ongoing role as Pharma Champion for this project.

Next Meeting Dec 12th 5pm UK time at https://ucl.zoom.us/j/97172937586https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fucl.zoom.us%2Fj%2F97172937586&data=05%7C01%7Cevert.homan%40ki.se%7C1c492cd74d5b428cbc4c08dac6fad591%7Cbff7eef1cf4b4f32be3da1dda043c05d%7C0%7C0%7C638041077877435568%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=UDIbxZnD6HU%2B16NJq%2F1gYjT0TlOpodUPSsqG5%2FGlNzg%3D&reserved=0

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mattodd commented 1 year ago

Sorry @Evert-Homan - my mistake, tagged the wrong team. You can ignore!