Open Source Antibiotics Series 2, 4 Jun 2021

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From YouTube: Open Source Antibiotics Science Update June 4 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/74
On the call: Professor Matthew Todd, Dr Dana Klug, Dr Edwin Tse, Giada Sabatino (UCL), Dr Jyoti Chauhan (NEU), Dr Chris Swain (Cambridge MedChem Consulting), Anthony Sama (Citizen Scientist).

A

All right, hi everybody uh welcome to the meeting on 4th of june. I just posted the new issue and and some comments about the last meeting we had um chris, you went there, but it was. um It was a mostly about the tox issue and alex um from the school of pharmacy posted some data on her analysis of the tox and the talks looked like it was pretty uniform across the molecules.

A

um So we didn't see, you know the the lower toxicity for the molecule that the lorry saw low toxicity for, um although of course the assay is different, so we were trying to figure out well. How serious is this and uh roughly how bad are the data you know?

A

Are they terminal or are they okay and we don't need to worry, or is it an artifact of there being lots of different assays in play here and so um and ellen daniel and and anthony if I've got anything wrong to say, um because I'm trying to remember from the exact watch, they're recording, um and so I think, the the the basic we what we do we did is we thought well?

A

Is there a gold standard, tox assay that we should be using for an antibacterial series um you know, are we are we all basically right or are we all missing a trick or yeah, which one should we should we be using, and um I emailed mark vlaskovic from coad to ask? Well what do they do?

A

um You know because of course, they've examined a huge number of series here.

B

A

And they said well as I've just paraphrased in the issue. There is no gold standard, they use um heck, 298 and hep g2, because they're from organs that are often associated with antibiotic toxicity um and the output of the assay can be very variable, depending on how you run it. But, generally speaking, they said if they, if they see toxicity at a similar level, to the antibacterial activity they carry on, which is where we are pretty much.

B

A

B

Way that makes sense, because there are some drugs like the fluoroquinolones, for example, uh that are pretty somewhat toxic or pretty cytotoxic, so it would make sense. I suppose.

A

Yeah, I I mean yes, the, I think, a thing that was being highlighted um by him was that often you don't get good correlation between in vitro toxicity and issues in vivo and that's a very general statement, but essentially that's the that's why the bar is quite low here. Yeah.

B

Yeah and they were saying that.

A

The the the more rigorous criterion for toxicity is about red blood cell hemolysis, which was.

B

A

For example, it was evaluated in the series before we started um and- uh and it was seen uh they see ten perc, so they they didn't see the sort of again the sort of artificial bar of 10 hemolysis of the at the mick, so so cena's sufficiently promising to carry on um now that doesn't solve the problem of us of us having a bunch of data which suggests reasonable toxicity, but it isn't at the moment, a sort of killer red flag.

A

I guess I got that roughly right based on the people who are at the meeting.

B

I mean well, I I don't expect these compounds to cause moles. Just because red blood cells don't have a nucleus, they don't have dna.

A

Right but you're making an assumption there, obviously.

C

Yeah, I mean anything that uh many compounds can cause hemolysis just because of their physical chemical properties. Anything that disrupts membranes or anything like this will cause hemolysis. Yes,.

B

Quaternary saltwood.

C

But no there's lots of compounds that are just um amphiphilic.

B

um But we're relatively compound slightly basic. I think.

A

Yeah yeah, but lots of different ways in which it could happen.

C

A

So I mean you know. The short story I mean so alex is finishing off her her analysis. She had a an incomplete table of data, which is fine. So from a publishing perspective. You know we need it to be complete, so we have a one analysis done by one person: there's a complete set of data, which is good, so she'll continue to do that, um she's willing to look into whether or not there is um an apoptosis mechanism of action. I think it was where we left it.

B

um Yeah, so I looked into this a little um further so there's this uh master switch kinase called atm, which is uh activated during dna damage, so what they, what what she should do or what I've seen people do in papers is they have a specially made antibody, that's already pre-made pretty easily bought it's been labeled with a floral for and it binds to the phosphorylated atm, which gets tripped when there's dna damage. So I think that's what's going to happen, I'm not sure, maybe follow up with alex on that.

A

I'll afford her the issue, I think you posted.

B

Yeah uh anti-phosphoatm uh fluorescence microscopy is the kind of generic way to see. If oh or is, is this really damn gd in it.

A

um Then, subsequent to the meeting laurie posted you just joined right. Oh yeah lauren just posted a um a comment, um so this is at the bottom of the c72 um around compounds for which they got um pk um laurie. Did you just want to mention the significance of this.

D

um So I thought that actually, the follow-up comment from ben was really helpful um and he pointed out a couple of um points in there that I I didn't capture in my comment. um I I guess I really wanted to highlight this. So ah thank you so much for posting that link map.

D

um So the thing that I um I found most interesting about this, um the two compounds on the left, so three, five, seven, nine, four: zero zero and the one ending in three five: seven, six from mrc five, both of those were seeing when micromolar toxic, what we would call toxicity um and yet, when they went into pk, neither of those compounds actually were toxic.

D

In the pk model. We saw no signs of toxicity. um Look full disclosure exposure. Wasn't super high. It wasn't high enough for us to progress into the efficacy study, whether that means that our exposure just wasn't high enough to have enough compound available to be toxic or to see toxicity. That could be one thing.

D

um We did also, though, uh like cordosis with abt um as a sip inhibitor just to see if that would also increase the exposure um it did, but not to a level that we were happy to progress into the leash efficacy studies. So I guess I found this interesting because it comes back to that point you made matt earlier about in vitro translating to in vivo talks is mrc5 the best-selling line to look at in terms of the top, maybe not um when you think about 3575.

D

That has a better tops profile overall compared to the other two that one was the one that we did see adverse effects in the pk. Our exposure was also higher. There was a question mark, as ben mentioned, in terms of whether um it was the abt that was kind of contributing to that as well.

D

So yeah, I mean, I think, there's still a question mark about the series as a whole. I think that for me this in this data, this information kind of suggests that we should keep going uh and don't jump ship just yet, just because.

D

Sorry, what was that.

B

So basically proceed with caution.

D

Yeah look, I mean, I think, once we actually get to the point where we've got something that looks really interesting and then we go into a pk with it. Well, at that point you know we'll have an answer as to whether or not talks is really an issue for the series as a whole. I I mean yeah.

A

Yeah, it's interesting his name. It's a complete uh lack of correlation for those three compounds. Yes,.

A

Just to make sure I've got my nomenclature right. um The compound that ben mentions, with the invitation for isle group, he's talking about the group with the nitrogen uh in the essentially the ortho position, which could um one two three understand but figure out where that is one. I'm trying to remember.

D

A

That, with a collating motif.

D

So the you replace the pyridine with the imidazole is that.

A

Yeah and the nitrogen is, is it? Is it collecting.

D

A

Trying to think of where, if it's next door to if there's a nitro next door, I guess that must be.

D

A

So um if I I hate no microchip but you've got the you've got the nh you've got the carbon. You've got the enemy yeah.

B

A wonderful um thing called opsin: uh ours isn't nomenclature into a structure. Vial.

A

You know no sure I just there's no excuses being chemistry, professor, I'm not knowing that.

D

I'm just going to pull out this structure just to triple check.

E

Yeah, I think that's right, because the um yeah amidazole's got nitrogens that the one.

A

And the only thing I can't remember is whether the one is where the um yeah it's potentially collateable, but it depends on where the h is the ex it can tautomerize. So it doesn't really matter right, but it's got the potential.

C

To be collecting.

A

Yeah I mean yeah because of course, those yeah okay, okay yeah, I mean the. The overall message is that we can ignore, ignore all the talks data we've got, which makes you think why we do it in the first place.

C

The problem, the problem is, of course, then that you and you're you're deciding whether, if you have any cox, is an in vivo assay, which is expensive to do and undesirable yeah.

E

Well, we have built-in funding for a pk study for the series right, yeah.

B

E

I think that you know, and then that would tell us whether we have in vivo talks as well. So I think my takeaway personally is that you know, even though, though, we're seeing this talk, I think that shouldn't stop us from trying to at least get a compound into um the in vivo pk study and then.

B

E

Will give us some more reliable data to go on because.

B

E

B

Said fluoroquinolones, for example, are somewhat toxic, but most people, not all people, but most people tolerate them.

B

Okay, so I wonder if that's almost similar to what we're seeing here.

B

I think I think.

D

Things are dude.

B

D

Yeah, I I showed the structure of that.

A

Yeah, oh sorry, I missed it. Sorry I missed it.

C

It was that's what, as we thought,.

B

B

And this was not that toxic in in viva.

D

Yeah that one, what did say again, um good exposure, no adverse events um that one was looked at for for charges, disease. The only concern there was that it's also a tea cruising sip inhibitor, which isn't that good.

B

I sip it was that one of the fanara balls yeah.

A

um All right, so uh I guess we proceed as planned with the with the synthetic targets I mean and then and then get a you know, full picture of the sar and then make a make a call. um I think, you're right dana I mean we do. We do have the ability to pick a compound, so we should bear that in mind um and and maybe based on the next round of potency evaluations that might inform which compound we're choosing there.

E

Yeah I mean, I think it's so good- that we've kind of done our due diligence with the um cell line talks yeah, so.

A

Okay, uh so yeah alex is working away on that we can invite it back, which is um when she's finished, to tell us about it. um I've asked paul stapleton for an essay slot um and I'm waiting to hear back about when he can evaluate the next compounds, um and then I didn't know if anybody wants to do update on chemistry. So flavio can't join us, but I know he'd be running away in the chemistry in his lab. um Did anybody have anything they wanted to say about compounds that are being made?

A

I didn't give anyone any warning, so no worries. If there's nothing.

A

E

um I was going to kind of get back to the one pot reaction with the five-membered rings that are on our list um and try and get enough of the alkylated and the unalkylated portions of those.

A

D

I know that chemistry at northeastern has begun. We had some issues getting one of the reagents in, um but that's now in hand, and so we're actually just trying a couple of different routes.

D

What we found historically, the an alkylation chemistry is that we get a mix of mono dye and dry alkylated materials which are really challenging to separate um even by reverse phase, and so um we're also changing up the order and actually putting that in first and then trying to do a block wall to get the um the four fluoro aniline like portion um installed.

D

So that's happening. We haven't got too much progress unless georgie wants to say something acknowledging that I've put her on the spot too. There, though,.

F

uh Hi, uh so yesterday we put a bookword reaction, so might be. Today we will get the result and, depending upon that, we will check like how we will change the root yeah.

A

Right all right, that's fantastic great! um I uh one moment I just had yeah so on the issue um that I just posted, so flavio did comment about: uh where should he post experimental procedures and data of synthesized compounds?

A

um So that's on the issue I posted just now. What should we do with that? So he I don't know if I mean the thing to respond, there is the thing to say there is if he has a lab notebook, he can put it there. If he doesn't, then what should we do with that we've? You know: we've got a github.

A

We can use as a lab book in a very crude way if people want to post things there or to their own lab books, or I don't know what what do you think um is going to be the best solution, let's say he's making five compounds. What should we do with that? um You know we can provide guest access to lab archives because we have a license.

A

What's the best solution, you reckon.

D

Could you post an issue with the structures and then attach a word doc um with the experimental or you know.

A

Yeah, I can do that. It's just it's. You know poor poorly machine, readable, that's all, but we can probably deal with it uh so difficult to find it. You know um we'd always talked about having an issue per molecule. You know and getting up and see if it works as a lab notebook, just posting smiles and stuff there and then dumping everything. um It should probably work.

A

Actually, um if you're happy with the idea that it it dilutes things a little bit um or we post it somewhere on on our own lab book and just link out to us that's a possibility, but um we could. I guess we could look into getting. If, if clary doesn't have an elm, we could look into getting a guest account. That's always possible right.

E

um If we put them into the osa spreadsheet and have a link to if he uploads his experimental to github, would that work yeah.

A

Okay, it would, I guess I'm thinking I mean because I don't know if he's you know, got a just a word file and then a bunch of um you know. uh Data sets, like um you know, essentially fids that he he's just got or whether he's got a as you've got a bunch of data, or has he got a write-up? I guess that's that's the thing I'm not sure about. So we can clarify that.

C

You don't have to have an issue for every compound. Couldn't you have an issue being a lab notebook? Yes, it'd be very big. Yes, you could, and then just have people add add to that each one. Each edition would be just a new page or a new compound.

A

Yeah, it's certainly possible. um I kind of hope that there was a way of using um projects as well and github is doing this- that you can set up a you know for the top right. It's got issues and poor request actions, it's got projects and I wonder if you could use that as a way of keeping something together, I haven't tried it um yeah, but um yeah I don't know um so.

A

I think I'll, try and reply to him, but but if people can chip in with advice on something that would be really good um also, I don't remember uh if, when somebody, I wonder if somebody else remembers what flavor you said about testing did. Did he mention that he was going to get him tested locally, or is he going to send them to us to get tested? I forget what he said.

A

I think he was going to send them to us right. I think.

E

A

Yeah, okay, fine! That's fine! I think that's what he's implying sorry! I think he's going to have some compound sooner to ship out, which is great.

E

I just sent a follow-up email today also about those amids, uh because I realized I hadn't heard anything back from the finance guys when we tried to order them. So I just gave them a little nudge, yeah.

A

Great, thank you. It was just a clerical thing right we're going to be able to order them. It's a credit card issue. I think yeah. Okay, that's good um and then add the metabolite you're done right, yeah! Okay, do you wanna just to update people.

G

Well, yeah, I mean it's hydroxylated on that methylene group, the bottom, which is what we predicted, I guess and um somewhere uh yeah. I.

A

Do have all the nmrs I've not uploaded them yet, but you can't do. Can you stick it on yeah? I mean just stick it on the issue: right, yeah, yeah, okay and then just highlight the evidence that which would show the change that would be great um and the amount you've got is like a meg or something right, yeah, so so a we. I mean we can't chemically mess around with that. um I.

B

Found something that could potentially allow us to abiotically make more of this. I and the reagents are very cheap. Do you still have the parent compound? How much do you have? uh We've got a lot of it because we made more for. Could you take like 20 minutes? Put it into dcm, add six megs of mcpba.

B

You know and see what happens.

A

Well, the question is whether it's worth it that might so. My my question was whether or not that compound is: um do we care if it's active, so the last.

G

Time I tried an oxidation with mcpba. It gave the n oxide. That was when I was trying to do the sulfur oxidations. So.

A

F

Sorry just remind me how much.

G

A

We send to a poll for potential evaluation like two minutes or something yeah like one to two. I guess, and so, if we had, I mean if we committed the whole milligram for potency, we could get a potency evaluation on the metabolite is that is that I don't know if that's interesting, I just don't know if that's actually relevant or important to know I mean I guess it's useful to know, always isn't it if a metabolite is active um chris, you know more about this than I do. What is there?

A

The advantage of having a metabolite evaluated? Is that you don't care too much about the clearance rate so much because you, you know you actually want to produce a different molecule.

C

Well, I mean it's a variety of reasons you might do it. One is from a more for a developmental thing that you need to know all the information on all the things um it could give you an extended duration of action, perhaps yeah, and if it's a metabolite that actually builds up, it tends to suggest that it might be more stable.

H

B

Do you think I mean because it's such a small quantity would I mean maybe on a very small scale, you could try different eye. You could try different oxidants and see if any of them make it or is that a lot of nmr? What.

G

I don't think it's worth it on what I have.

A

No, I mean, but we I mean if we have the characterization data for us and we're done, um then I don't see a problem with sacrificing it for a ponzi essay.

C

Yeah I'd agree with that yeah. If it turns.

A

C

If it turns out to be super potent, you can always you'll be more willing to go back and make more of it.

A

Right, there's your incentive.

H

Yeah, I mean that's true.

A

Okay, and and are we able to accurately assess how much we have I mean, is that, like a milligram, we need to know roughly how much we've got? Can we accurately assess that uh yeah.

G

So I mean it's weightable out so yeah way.

H

G

H

A

Okay, great, I think that that would be a good use of the compound and getting extra value out of the fact that it was quite a large scale procedure in the first place. So there's a reason for doing it.

A

um Okay, that's great! uh Well done! That was a campaign um all right. I think that was everything I wanted to mention, because we've.

B

Covered everything.

A

I can see anyone got anything else they would like to report or ask, or mention.

B

I didn't totally hear about the amites, so they are commercially available. You said you can get them.

A

Yeah, it's just a financial glitch and that's all we just we just got to push it through, but we'll get on. Do we have any idea when the next potential.

B

The next sarah val will be, you know next part of the season. No I'm guessing next week, maybe.

A

Okay, so I guess we're yeah should be okay, it depends when uh paul is next in where the building is very mixed occupancy at the moment, so it's all of it. uh I can't just come in whenever you want. You know.

A

Still all right, well good stuff, in that case I'll, try and post the uh recording and action items and stuff. Okay sounds good great nice to see everybody thanks for coming along all right, see you again soon hi everybody bye.