Open Source Antibiotics Series 2, 5 Feb 2021

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From YouTube: Open Source Antibiotics Science Update Feb 5 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/54
On the call: Professor Matthew Todd, Dr Dana Klug, Giada Sabatino (UCL), Dr Chris Swain (Cambridge MedChem Consulting), Lee Graves (UNC Chapel Hill)

A

All right, good afternoon, everybody uh or morning, wherever you are uh it's friday february, the fifth and this is open source antibiotics series. Two and um today we are gonna, be talking a little bit about mechanism of action stuff I think and um talks stuff as well, and what we might do about some of the talks data that we recently had. So um if I just share screen and bring up the the current issue.

A

Hopefully that is, that is all clear: it's the february 5th great um and uh we don't have any. You know new chemistry stuff to report, because there's nothing going on the lab just at the moment, uh dana's back in that pretty soon, um and uh we have some compounds that were shipped from the lorry which um we will get evaluated by paul stapleton.

A

I think next week, end of next week, so I think he's he's happy to evaluate those molecules um that were that were contributed, which is great, um there's only a few of those like six and but he's happy to do it because he also wants to um do an evaluation versus um mssa which, as I understand it, is uh lacking in any flux pump.

A

If I read that correctly, dana in the email um or in other words, he's trying to figure out if one of the reasons why we've been hitting a potency ceiling, which we spoke about last time, is because of efflux, which I guess is completely possible right, and so he was saying well, he could do that at the same time, and he was saying um you know: do we want to re-screen some compounds that we looked at previously versus mssa um to see if that's an issue, to see, if there's a difference in potency- and he was asking us in you- know in that case- which compounds?

A

Could we have a look at again? So I was just thinking about this earlier um sorry, we'll get to your stuff in a minute like I just wanted to cover this. While it's a refreshment, um the the issue really is you know which compounds? Might we want to send to that? Now? Obviously, we have to put in the usual positive and negatives, which the positive is um 81., which is our uh lovely.

A

um Here this guy 81 as normal and 820 as the negative control. Obviously, but then my thought was to put in some molecules that um I guess is a gut gut feeling here. You know molecules that maybe gave a sniff of activity but weren't that impressive um to see. If there's an improvement, you know in the absence of an efflux pump- and I was thinking particularly of um some compounds, perhaps with with a mean side.

A

Well, I was thinking about the parameter here 865, which has this this parameter here, which gave us a 4 which isn't terribly good, but I was also thinking about some compounds uh which gave a sniff of activity with perhaps some amine functionality. So perhaps there's eight five one with this aniline here, which gave us an eight um and maybe this, uh what was it? What was?

A

I thinking, I think, eight four two which has an amy, so this guy with the eight the benzoylene just because you know, as we know, you know what primary amines are supposed to be best for um avoiding efflux according to the entry criteria, and so we we could reasonably expect better activity with those.

A

Perhaps just before I ask anyone to chip in here, I guess the first thing we could do is to put a representative set of these molecules through the the algorithm on the hergenwalker website to see whether or not they are predicted to behave well against efforts.

A

That seems like a sensible thing we could do, because then we can have a measurement of globularity and planarity and all those things as well as whether or not they're they have primary amines.

A

um Anyone want to suggest anything about that, because it's an important test to do.

B

Obviously, could we try the dimethylatiline, the dimethyl uh amide that we had that proposed a while back? It was pretty, it was to put a polar substitution went on, but it was not held at all.

B

It was on the top end of the molecule there's a para para-dimethyl acetamide functionality right am. I.

A

A

This table is complete right.

C

No, uh no, it might not be on there yet sorry matt. uh I think it's missing the very most recent one, so I'll try to update those.

A

Thank you great okay, because that could be another possibility and of course you know, I'm assuming we've got these in-house and we can just you know, providing the poor. uh Obviously that's important, we don't have one, then we don't have to include.

C

Yeah, I think paul his email implied that he had still has the stock that he used originally, but we should confirm that right, okay,.

A

Okay, great um one uh dana: are you happy to so when you're putting these on the sheet here? Would you be happy just to put in I'll I'll put in a comment in the in the issue which molecules I'm thinking of um just so? We've got a record of that and then, if you could just put those in the hogan wrote the website, so that means getting the smile strings and then just pasting them in there and getting the feedback. The report back for those that would be awesome.

C

Yeah cool yeah. I agree I was thinking the paramethyl also and then a couple of the um nitro the n length cores. So I think that that's a good idea. Okay,.

A

All right, um that's great, and then um the the other thing I was just going to mention quickly is uh where's the talk stuff. So we uh we have the data from uh lori's group on the toxicity of some of the compounds that were sent over, um and I guess um I just want to bring this up because.

A

Yeah, so this is the day you just posted a few days ago or anything um and we're looking at um mrsa uh mick and then toxicity uh that we had a little discussion about um about units and stuff, but so you've got. You know some some points again. Quite you know quite low levels of potency for the compass that we know about, and then we've got the toxicity over here, and I mean to my mind, that is not a big window.

A

um You know we're not seeing huge micro molar values for the for the for the uh mrc 5 line versus mercer, um and so you know we need to wait for for the potency values for the remaining compounds here, for which there is toxicity for some. You know it varies again um and we need to wait for andreas's group to finish their assays, which I think they'll they'll be able to provide us with the next meeting. I think I think I'm hoping they might come along and talk about their values. I think we'll have those.

A

Finally, those talks values for our representative set of our compounds. um I.

B

I was gonna say something though uh there is another thing that you use at mic is visual growth on plate, there's something called uh nbc or minimum bacteriocidal concentration, which uses a cell counter, and that would be in the same u.v and micromolars.

A

um Lori these are, these are numbers that we got from you right. Did you have any? I mean when you look at these. What were your, what were you thinking about these? They look slightly worrying to me.

D

Yeah, so this was our concern um and this was I'm sorry. Can you zoom in just a little bit I'm just trying to differentiate the numbers on the um image.

D

Clearly, my screen resolution is not great, um so I think eight five, five and 980 for us was kind of a good comparator and I'm just trying to see 855 and 980. Yes.

D

So if you look at that, this is one of the things that I was talking about, where the them and admittedly they are, they have more than one difference, but we have a number of matched pairs, which kind of have a similar trend where, when you flip the position of that methoxy, um you actually see a big change in terms of your toxicity profile and so we're really pursuing kind of more of the like 980 sorry, the 855 um related scaffolds, where that methoxy is, I think, that's the sixth position um so for us, that's definitely been better.

D

So I mean we've been able to modulate toxicity against some of these cell lines by flipping that substituent position.

A

Right, obviously, 8.5 doesn't have the collecting pyridine of it.

D

A

um And I didn't think to try to track that, but that is the only content which doesn't well a56 right um this guy up here. My my I'm hoping you guys can see that my zoom stuff is overheating. um That actually 856 is not bad and and it's got the same thing um in terms of talks.

A

D

So actually it might be that eight five, six nine eighty might be the better comparator. I'd have to go and double check really quickly. Okay,.

A

Yeah I mean I guess I wanna wait for the data to be filled out here and in our other set, that's being measured in-house, but um we've got to keep an eye on this because I mean if, if we're not, if we, if we get all the data back and we don't see much of a therapeutic window, then we've got an issue.

A

D

Yeah, but for us I mean we found that um the the position of the substituent on the scaffold, okay, um that really impacted potency against or toxicity. I should say.

A

Okay, that's really good to know.

B

Again, we don't necessarily need a substituent in that position. Do we.

A

um Yeah I mean, I guess I'm just uh I'm just any any trend that that mercer potency is tracking talks is just something we don't want. Really that's it, but.

E

Some of these are quite difficult to rationalize. I mean if you look at the series 981 982 983 979, at the top right, all what you going is just different alkyls on that nitrogen and you have 983, which is relatively benign and then 979, which is just linking those two methyls together, is much more active, much more toxic, so it doesn't look like well, it's either.

E

Very small changes make big differences or there could be quite a bit of scatter in the assay.

A

A

Right true, yeah.

A

A

Yeah, that's a good pair. Actually, isn't it.

A

A

um Okay, good, so um we will revisit this, I'm sure you know when we've got more, but let's keep an eye on it and we have to keep an eye on it as we go forward.

A

um Okay, I wanted to quickly move over to um mechanism of action because we were obviously talking about this previously and which, over the last time and then and then leaves with us, which is awesome, so um the you know just refresh people's memories.

A

We had this list of interesting looking um targets last time which we were starting to think about a little bit and uh and dana posted the the sheet which you know reveal you know show these four, maybe is the most interesting because we had a kind of you know down regulation of a significant degree versus these guys. These are on a lysate where, as I understand that you know you have the the thing is lies, and then the compound is added, so there should be no necessarily functional connection between anything because we're not exactly.

A

We haven't, got functioning pathways anymore in the lysate, um and so the question is whether or not these are interesting targets. Now you know lee you were mentioning before about you know doing this again with more protein and stuff, um and we had a few other discussion points here. Did you want to did you want to say about these now.

F

Yeah- and you know, I think we were looking for dose-dependent changes. Obviously um I went back and looked at the data and I thought well, there are a couple other proteins in there. It didn't show dose dependent competition, but they did show what looks like 28, specific competition and not 26..

F

That was the hiss s, protein idh2 and then trmb. They all all three of those proteins showed uh a decrease, although it wasn't dose dependent, so I initially had sort of toss it out, but since it's a lysate it may be that we're already at the point where it's bound and it's competing. So I thought about. If we repeat this, we should do it with lower concentrations of maybe a larger concentration range and more protein to start with, so that hopefully we'll get more targets, so we can set that up.

F

I think that's um as long as we have compound. I think we still have 26 and 28. I'll just get another batch of mercilysate and we can. You know we can maybe discuss what the concentration range should be, but I think it's worth repeating to see if we can repeat some of the data that we have and then maybe extend it a bit as well.

F

Don't know um any other thoughts on dana did you have any other thoughts on that.

C

um Yeah, I think that sounds reasonable and um it'll be good to see if also these, the two that we're looking at as being interesting, show up again, um because that would I think that would be really good to see um but yeah. I think that would be great.

F

And I was gonna: have my tech replot the data, so it's easier to see he's got some of it really crammed into some of the. I want to break it down. So it's it's more visual and I'll work on that, so cool.

C

That'd be good.

F

But I think we have to repeat it. That's just the way it is. You know.

A

Okay- and I I didn't want to ask you this- you know put you on the spot, but I mean obviously you're hoping that that isn't too much of a financial button right there.

F

A

That would be fantastic um and uh the I mean in the meantime, so uh giada's been looking at whether or not any of these are. You know known targets right with with magically a someone you know around here, who's running an assay, an enzymatic essay or one of these things already. um So I guess that's the search, that's ongoing to see if there's something that we could just have a look at in the meantime, um and I guess that search is carrying on right. You're still looking at some of that stuff.

G

Yeah um I I'm trying to find something because it is not really um I mean it is not like you search something, and then you find what you are searching, because sometimes uh names are not really the same. So I I need to read a lot of papers and then try to see if I I find something, because there are not not a lot of things regarding safety focus areas and and enzymes, so maybe I find something that they belong to different classes, but maybe the same so I have to do more. Research.

A

All right, great yeah, no, I mean it. It can be very difficult for both terminology and just because complexity and information so welcome to the research community yeah. Thank you.

E

So have these two compounds been in the toxicity essay.

A

That's a good question.

C

No, we, I I'm pretty positive that we gave we they we included them in this, set that andreas has, but um the mrc5, those those are the that's the data from uh lori that she just had on her. So you don't have talks data on them right now,.

E

Okay, that's a shame because it might also be in a way of us telling what the toxicity was due to.

A

Hopefully, next week will happen. Yes,.

F

um Do you think we should wait before we do our experiments to find out the talks, data.

F

Would that change your interest in those molecules per.

A

Se good question.

A

I don't know um I mean they're, still, it's still positive and negative. Isn't it at the moment? Still we have a positive and a negative, and we we aren't seeing a total track of potency with toxicity.

C

I guess I don't know if um how much more work this is for you lee, but maybe if the tax data would make us um lean towards, maybe throwing in a third compound. If you know, maybe if the active is toxic, but we have another one, that's active, but not toxic. That would be maybe more interest, but I think you know we would still want to keep the original control in there just to be able to sort of see how the experiment compares is. Is that it's not a lot simple.

F

Okay, just we line them up and we add additional set of samples that wouldn't be that hard.

C

What I mean, what do you think that would that maybe be worth it then to wait or no you.

A

Know I don't know I mean if we're going to get the data next week on talks. We can wait a week.

C

F

Okay, yeah, I think that'd be great yeah. Okay,.

A

All right, good, um there's a other question. Maybe it's naive, um I I was just suddenly thinking you've got you've got the the mercer lysate coming from a lab, that's somewhere nearby right- and this may be my misunderstanding- this whole field, but but in in malaria, drug discovery, you grow bugs that become resistant to your drug by giving it at low doses. And you wait for you know, tolerance to emerge, and then you sequence and you find out what the change is. Can you do that here with masa?

A

Can you grow bugs in the presence of a drug and see what changes genetically.

F

F

Yeah so there's a guy brian conlon who works across the street from me, he's a you know, mrsa expert and they they grow this stuff all the time and um they were kind enough to prep some cells for us and give us uh the lysate or give us a cell. We made the lysate from there. Okay.

A

And I mean if you're in conversation with them, could you ask them what would happen if we grew the bugs in the presence of the positive here? That's right.

F

A

F

A

I mean, I don't know you know in malaria, it's it's a pretty, it's a pretty good experiment. It can't take a while. It depends on on the compound and the target, but it can take a while. But then you you wait for your ic50 to shift by you know, factor four or something and then and then that's intolerance and you sequence it and you find out what it is. I'm assuming you can do the same thing with bacteria.

E

I think they have bacterial lines with no mutations that cause resistance, which they just screen against.

A

E

So I think that they already have many of the mutations up front.

A

Right, you mean maintain somewhere for uh yes, the outside.

E

A

That would be a very nice right that way. That would be better quicker, yes, yeah. uh If anyone knows of any place where we could send compounds over and have those evaluated against a bunch of common mutations, that would be amazing.

E

Yeah I can ask about that, but uh because I know companies that are working in this area, I don't know whether there are public resources that you can access, though, but I will find out thank.

A

You that would be very, very interesting.

A

um Okay now I think that that was the that was pretty much everything, um because everything else is on hold, which is fine. um There was this thing that came up just in the discussion, so mike with an extra eye is, has been a contributor to some of these open projects for years now and he's a he's a coda guy. um He was interested in this idea about why uh spreadsheet wasn't indexable. Does this make sense to you chris, or is it still unresolved thing here.

E

As far as I can tell, the sheet is accessible to everybody on the internet, so but there may be some subtle permission somewhere that I'm not aware of.

A

Okay, okay! Well, we can keep over dialogue with mike um yeah he's very happy to help and it's his expert on technical thing. Yeah.

E

Well, I mean he has access to the spreadsheet. So if he knows how to modify the permissions, then you should yeah I'm happy for him to do that. Yeah, okay, yeah sure.

A

Yeah, okay, those are the most important things and I think that's everything I want to talk about anybody have anything else they wanted to mention or raise.

F

No thanks thanks man, we'll wait till you guys, get your results and then we'll prepare to start it over again great.

A

We'll let you know brilliant, that's fantastic, yeah, all right thanks! Everybody thanks for coming! Thank.

E

A