Open Source Antibiotics Series 2, 2 Jul 2021

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From YouTube: Open Source Antibiotics Science Update July 2nd 2021

Description

Weekly open project meeting for Open Source Antibiotics Series 2.
Full Project: https://github.com/opensourceantibiotics/Series-2-Diarylimidazoles
Relevant GitHub Issue: https://github.com/opensourceantibiotics/Series-2-Diarylimidazoles/issues/81
On the call: Professor Matthew Todd, Dr Dana Klug, Dr Edwin Tse, Giada Sabatino, Dr Alex Vaideanu (UCL), Anthony Sama (Citizen Scientist).

A

That's green and stuff: okay, so welcome to open space and verdict series two friday, second of july three minutes past two- and I'm just gonna- share this because it's the um relevant thing so just while we're waiting for anyone else, because I think I want alex to kick off and just tell us a little bit about what she's been measuring for toxicity, um I was hoping lee would be. Lee graves will come along today, but he can't make it.

A

He just messaged me so he's going to come to a future meeting, but they are um they're happy to re-do the experiments that we have been running uh with them to try and identify a mechanism of actually a target for in mosa and to look at mammalian cells in parallel, um and uh so he's gonna I'll I'll, be in touch with him by email and he'll come along and chat about it at a future meeting.

A

um But just to give his sort of apologies for today he was hoping to make it but can't, um and then we'll do chemistry in a minute. But um given that alex's is here, we can cover uh first. That would be the the best way of doing it. I think which I'm just trying to figure out so um alex if you are happy just to describe a little bit of what you're doing. That would be absolutely awesome.

B

Yeah, um maybe I can just share the screen with my previous uh slide and donate.

C

B

That um yeah so last time I participated in this meeting. I'm sorry, I don't make it every time. um It's fine! I I showed you that uh I looked at toxicity many different ways. uh So, first uh we did the quad protocol, which just involves the rest of the ring assay and then culturing the cells for 48 hours, a treatment for 24.

B

um I did exactly the same procedure using mtc as a readout, and I've discussed the differences between those two and we also looked at a one week protocol where we seed the cells we allowed them to grow, to exponential phase, treat them and then also allow them to recover after treatment so uh from comparing all of those things, um and I've done this for majority of the compounds that I've been given, not all of them. Yet.

B

um So what I can conclude from this is, irrespective of whether it's wrestling and or mcc, we get fairly consistent values. Definitely the absolute values are not the same for the ic50s, but definitely the trends are the same. um There are for the 48 hours protocol, the data seems to be more variable um and there could be various reasons for that.

B

One is the growth of the cells is. If they are not an exponential phase, then it's more variable um so what I've been doing since then. I compared this entity readout with the one week protocol with a recessor in readout, because I had this weird uh value for the 48 hours when looking at the res hazard and mtt for the 983, which is a very interesting compound uh for us, so um yeah, comparing the readouts here for the one week protocol the data is a lot more consistent.

B

So, as I said before, I would trust more this data than this one um and yeah I'm working towards sort of filling out all of this table, and I do I have collected more data towards that. But um yeah I haven't been able to plot it. Yet sorry so, uh but the trains are the same. The ic50s are between sort of one and four microgram per ml, uh one and four microgram per ml. Yes yeah! So that's sort of micro, molar uh range like tens of micromolar right.

A

Great okay, thanks- and the aim here still is to just complete this table for publication purposes, so we have a full set of data, um and if and if and when you've got that um we we just- I mean for the paper, we need the the excel and for the website we just need. I mean the same thing really, but but something we can put in the wiki. That indicates what what the values are for each compound.

A

um That's great, okay, and so I mean ultimately so far, there's no big changes observed, but um so we don't we're not being alerted to some significant difference here. We're still dealing with roughly the same figures: yeah yeah.

B

So they're more toxic than they are potent. I guess that's that's a concern.

A

Yeah yeah right right, yeah yeah, we um yeah we've got an eye on this for the um and just to summarize a little bit about what we were talking about before we came online here, um there's the possibility we might be able to do, provided we've got the resources in time. Do a quick and dirty dna binding experiment, but you might be willing to look into whether that's feasible in the in the short term.

A

Yeah. That's great! Thank you. um Yeah.

B

Sort of so I think the the two well, I don't. I don't know how. Many weeks ago we discussed that I would look at apoptosis, but so I mean whether that is going to tell us what the mechanism of action or not it is then it's not a given, and so and also it would take me quite a long time to do that.

B

um So we thought that just checking dna binding sort of more- I guess in silicon rather than in vitro approach, um would be um a good start and it would be faster and especially if you want to publish quite soon.

A

Yeah my so my view on that is. We should do the um the experiments at north carolina with lee and see what we get and then, if we get something out there, that justifies more work by you to to tease this this out, then we should do that, but let's wait for those experiments which are gonna happen anyway, and that might help us resolve some of these things.

B

So, what's the timeline for that.

A

uh I don't know I was hoping we'll be here, but hopefully I don't know actually well that's a good question I'll I'll. I'm I'm in touch with him already I'll be in touch with him again.

A

um I was hoping he'd be here, but he couldn't make it, but hopefully weeks not not certainly not months and probably not days, because that's a bit optimistic.

A

um Just yeah just the thing that we mentioned on the previous call as well about submitting compounds to the nci cancer cell line. I think we should look into that because that used to be a big deal, and I haven't submitted anything ever to that. um But we should probably think about that right because, as andreas mentioned on the other called the pattern of of potencies, there can tell you something about mechanism. Then yep.

B

A

So if that's still operating, we might be able to to do that. I mean it's. You know it's always simple, for open projects to ship molecules, because our mtas are either very short or non-existent.

B

Cool I I haven't personally submitted anything yeah. I think js knows more.

A

Yeah, okay, right, okay, good! I think my colleague zoe waller has, um if, if memory serves so I might, I might reach out to her or andreas and see how difficult it is great. All right! Thank you for that. um You're welcome to stick around or or go and go do some research if.

A

um Okay, I'm gonna share a screen again just to run through a few things, um so the I mean, I guess the one thing I think I I really wanted to do was to um run through the new acne data, which I I haven't thought about. So I wanted to do it fresh now um which came in and which has been plotted very nicely here by dana.

A

So we have the new data here for solubility and clearance, and what have you?

A

uh Okay so lots to do here, thanks for color coding it because it's it's there's a lot wow um danny you've plotted this. Did you have any immediate thoughts about what this might be telling us or trends.

D

Well, um I thought um 974 was interesting um because obviously it's admin properties are quite good, although it's not active um and then also taking a look at 864, it's not bad, um and then I forget what the osa number is, but the para cyano compound, I think, is fairly active and I actually don't think that we've evaluated that one. So I think that that might be a good one to take a look at in these essays.

D

um If I can coordinate with lori and see if she has bandwidth to do another batch of these, I think we should definitely include that one.

A

The wow, the potency, uh is all associated with high clearance right yeah.

A

huh That's probably telling us something.

D

um Yes, well, I guess the other thing to note um that I think anthony you pointed out is that most of these are the five five which we've already you know, looked at and found that it does get metabolized on that core, um so also potentially including some more of the five six. The fully aromatic core compounds to see. If that trend.

D

I mean so: we've got like nine seven, eight, nine, eight, seven one and then the rest of them. I think, have the aliphatic core right.

A

All right, okay, because clearance of 978 in the top left there is still reasonably high without.

C

There's also got a chlorine on the on. The core, too, could be, could be kind of being conjugated with glutathione or something maybe.

C

Right, we usually don't have any substituents on the core on that side.

D

And you know what actually should do also, because um we also got measured log d on these, which I actually didn't put in here, but that that might be interesting to take a look at, um especially in terms of looking at like 974.

D

I think I'd be now that I'm kind of coming back to it very curious as to whether that's actually got a lower log d and and if that's maybe contributing to its better admin properties. If we can maybe try to incorporate that into kind of design of compounds going forward.

D

uh That would be good to know so I'll I'll. I can update this. You.

A

May put it on the same diagram.

D

A

Yeah that'd be useful yeah I mean the color coding is really handy.

D

I'm pretty sure I saved it. I hope I saved it.

A

um Just on the solubility, how this doesn't look right right! This are some of these salts. Is that what's going on because it's 97976 right, there's like a two orders of magnitude, different solubility and it's it's just I mean I mean all of the ones.

A

I wonder some of these assaults.

D

um They it should, I don't think, we've really synthesized them as salts.

A

I mean wait these, so these were these were sent by us.

D

Yes, these are all ones that we've made.

D

A

How can it be so different.

D

um But this is.

A

Just saturated.

D

You're talking about nine seven, eight versus nine seven, six.

A

Well, for I mean just, for example, all right, but I mean okay, what's a better pair, um let me see I'm trying I'm just looking at one where you've got the ap solubility above you know in the sort of hundreds versus one. That's like three and it's not that different. Is it okay? So the two wait: wait, wait, wait: yeah, 974 and 876.

D

A

Also, look at the solubility.

C

Difference between the sulfone and the sulfoxide on the bottom.

D

A

D

A

Yeah, I'm just I'm trying to I'm just thinking about once. You've got single digit versus hundreds and, and you think, wait a minute.

D

Well, for the for 974 versus 876, I think actually, log d would tell us something because I wonder if that is maybe ionized at physiological ph or something and that's helping.

A

Well, but so I'm just looking at some of the ones with the in the hundreds and they're the ones, with the kind of green clearance.

D

A

um That's not uniform, but um but yeah the log d might be relevant. There.

D

Yeah, I think that maybe log d is driving some of that sorry, I should have put it on here. That's right! That was a lot.

A

D

Oh, I can add it I'll update.

A

Okay, um because I mean again, there are, there are some um with nutty clearance rate and and some with amazing clearance rates, and that and that's really yeah.

D

I think the ones with really good clearance are the ones that are usually not active. Sadly,.

A

Sure, yeah yeah interesting okay, um now these were um these measurements were contributed pro bono right. Yes, so if we wanted to um send in some more recent actives without the five five ring system, we would need again to ask for a favor.

D

Yes, um I can check with lori about that. I think probably they could do it, but um yeah. We should ask before we just assume that that's possible I'll see what their bandwidth for that is.

A

Okay, all right great they're, very nice to have.

C

C

They were interesting too, because some of the inactive controls were actually really active against lash.

A

Did we um so I was looking for that sorry? Did we post that I missed it yesterday.

D

Yeah it's on the dndi issue, so it might, you might have to scroll down.

D

uh Yeah, I keep.

A

Going it's that one 60.! Oh! That's! Why right all right! Fine, oh yeah! Okay, great! uh Okay! I'm happy to look at that too. um Now, if that's useful, it's.

D

Yeah um I mean so. I had a little bit of a chat with laurie about this a couple of days ago. um She just caught me up on the phone um and, yes, she said they are interested in some of these for leash um and what their sort of plan is now is to try and put together a new target list based on um this data, and then she said, she'll share that with us.

D

If there's anything, we have that's similar, um I told her we're happy to send to her if we have stock- and she said also, if there's half, if there's anything on that list, that they're planning on making that we're interested in, um we can tell them and they'll, make a little extra and send it to us all.

A

Right well great, what's um what's good versus.

D

You know um for leash, I I would say less than I think five micromolar is is considered good, good pokemon.

C

820 is totally inactive against mrsa, but it's got a 2.0 micromolar against t cruise eye and leash.

D

Well, even yeah I mean even some of these are sub micromolar against leash, which I think they're pretty interested in yeah, because you don't see that often.

A

It's like 300 nanomolar,.

D

Yeah yeah now they are also showing some toxicity in these two cell lines, but um I think the level of activity is such that they're still, you know compounds of interest for that.

A

C

Better than amphitheaters and being penta sam.

A

Daniel, if you, if you were happy to do color coding.

D

A

On this yeah, could you- because I bet there's something screaming out here- where you've got little toxicity but bird activity, yeah, so yeah, the same kind of greens and ambers and orange reds? That would be fantastic.

D

Yeah, I can see that.

A

Wow um and and obviously, if anything in the toxicity here screams out against what we've seen so far, then we should pay attention to that too.

B

I'd say it's consistent, yeah.

A

B

Okay, eight six.

B

D

Yeah, I think that most of them that are showing um lower talks in these assays are the ones that are not active against mrsa.

D

If I just remember my impressions from kind of putting this together.

A

And again, the the talks appears to be tracking with potency just on a very, very yeah.

D

A

For mercy yeah, I would say so I mean here too right so you're getting yeah yeah, yeah, yeah, yeah.

A

Right- okay, all right so, but but color coding would be great, very fantastic. All right, great yeah, thanks yeah.

D

And yeah any northeasterns are interested in that, so we'll just obviously keep in touch with them about it. Okay,.

A

All right, uh great okay, so I mean those are the main things I think um the moa the talks, the admin data and yeah the link up with those compounds great. um Does anyone have any any chemistry updates? They would like to share with everybody. There's no need to unless you've got something you want to say, because I know that we've got things cooking at various places.

A

Okay, I'm assuming just things are, I haven't included anything new here because I think that everyone's working on things- and we know what we're doing based on last time.

A

uh So that's fine yeah.

E

Can you hear me okay, I think I um I got the product from uh the reaction that I started.

E

uh I think uh last time I showed you a slide, so I was doing a purple reaction for obtaining the first compound for the not world northwest um a mine substituent, and I think that I got the product, um but I have to check this better um yeah yeah.

A

E

You're talking.

A

About this guy or this guy, with this guy.

E

A

All right great, well all right! Well, there's a teaser! So once you've got the nmr we'll believe you.

E

Yeah, I I yeah, I know yeah, I'm waiting there, no more yeah.

A

That's great, okay, all right great look, I think. That's, I think, that's pretty much everything um there's all the key things. Anyone got anything else they want to mention.

A

Things are all happening all right great if anyone's got anything else. That's great thanks for coming on everybody. It's our virtual meeting and um uh we'll keep everyone updated and see you next time.