Open Source Antibiotics Series 2, 18 Jun 2021

Previous Meeting Next Meeting

⏯

youtube image

►

From YouTube: Open Source Antibiotics Science Update June 18th 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/77
On the call: Professor Matthew Todd, Dr Dana Klug, Dr Edwin Tse, Giada Sabatino (UCL), Dr Flavio Emery (University of Sao Paulo), Dr Jyoti Chauhan and Bruno Quiroga (NEU), Anthony Sama (Citizen Scientist).

A

Okie doke hi everybody, uh it's friday, 18th of june 2 p.m in rainy. London really really is raining a lot more than it should be by by a big margin. Okay, all right. Hopefully, everyone can see the screen.

A

So um thanks for coming along everybody, um so the I mean the main item of business is, um is, I think, to just try and get some meaning and learning out of the most recent potency data, which just came so um from paul stapleton, which is really good. So here we are um with the various bits of bits of data that came in, so the positive controls are kind of as expected, roughly they're performing just fine, um and then we saw the.

A

The first thing is the easy conclusion, which is the metabolite that we receive from haifa, the structure of which add elucidated with the oh here is inactive, so I guess we don't need to worry about it again.

A

It means that the metabolic clearance is of course important, because that could determine whether or not the drugs any good um if it's being cleared to something which is inactive.

A

um The five six core over here- I guess this is- I mean this- is just the you know- compounds with with this extra bit here and you separated these out as the 5 6 core. I guess this is just with this ring fused ring with a direct link to another aromatic ring right.

B

Yeah, it's just like the positive ones, but just for the six-membered ring right uncertainty right.

A

It's a direct comparison between that kind of thing: right got it: okay, sniff of activity, but nothing spectacular um and the other conclusion, which is really straightforward, that it benzemitazoles.

A

I mean that's disappointing, said today that nothing's happening right good to have done, but nothing's happening. So we can de-prioritize.

A

um I guess in the paper we might want to you know make you know include one compound, which is a direct analog to to an active compound and say you know this change, reduced activity and several other compounds were equally an active kind of thing.

A

um And then we have interesting ones. So the n-linked and n-methylated compounds here, um which saw some interesting activity with just with the simple substituent here with the paramethyl and in particular this value of two, where you got the n-methyl and the fluorine here.

C

What was interesting about this compound, I felt was that it had that that ring methoxy, that annoying you know methoxy of doom or whatever, and it was still potent so I think from the star table. I think it would be a good idea to keep the uh that methoxy pyridine, but remove the ring method, remove the bicyclic methoxy of the ring. You know good dude chop that ome off just keep video make a version of this compound without that, because maybe that will break the potency ceiling.

A

um The va, I think it's something he's checking uh next time. We do potency putting this back in, because the 8288 makes me a little nervous.

A

uh Real dip, I mean increasing capacity just for mercer versus the others, um and obviously the compounds that we were interested in previously. We were talking about the n alkylation of some of these things. We were interested in exploring the alkyl group, quite specifically right, so I guess um I mean anyone from northeastern on the call sorry, I've lost my my gallery view wanted us comment on the the groups that are being put on the nitrogen for the analysion chemistry. It is the the longer chain right.

D

Yeah, so uh we are working on iso but trial, one yeah and we are like optimizing, the reaction. The problem we are facing is uh we are getting two products: uh mono, alkylated and bess alkylated, so that we are trying to like those are not easily separated. So we are working on that. Besides that we are also working on protecting this end with the tertiary, but oxide like tertiary, butyl one so that we are doing with other root and we are getting product to.

D

That is positive thing, but we have to optimize that reaction because, uh like first we have to like initially we are getting 10 percent, so we are increasing the reaction, condition like to get a better yield. So we are working on that. What's.

A

The reagent that you're using to put the group on the nitrogen.

D

So you want to see the like screen, I'm sure I should oh.

A

Yeah great you got something: yeah that'd be great yeah.

A

If you, you should have privileges.

A

A

D

So initially we are working to make these kind of alkylated with most important one.

D

So we start our reaction with like simply protecting with cesium carbonate in dms and the problem is, we are getting multiple spots. These two are most important which are identified by the mass lcms and they are very close. We are unable to separate these with various method, so we are planning to like move forward beside that. We are also working on like first making this alkylated and then do the book to like related this one.

D

So in this we are optimizing, the reaction we are getting yields, but those are pretty low, so yeah we are working on that.

A

C

Why are you using the uh ied, iodide alkalinize posts, the alkyl chloride or alkyl bromide? Could that possibly be? Why? Because it's just so reactive that it you're getting plots.

D

Okay, so yeah this one is like we already like to optimize this reaction with methyl one. So that's why we are using um iodine, but yes, good suggestion. We can like think about chloride and bromide, so we can reduce the reactivity and the basic problem might be because of this thing, these two are like too close to like bulkier and close cavity. So they are like hinder the attack of um alkylation because one of the product we are getting with the salt with pyridine one. So.

E

Yeah yeah, I was asking this. So are you sure you are alkylating the this nitrogen between the heterocycle and the benzene and not the the other pyritine group? So it you don't have the base alkylated nitrogen, but you still have the the monoculated, nitrogen and the pyridine also alkylated. So what.

C

E

Com yeah: what are the conditions? Are you using like temperature? It's room, temperature or low.

D

Also yeah, we are using 55 degrees celsius temperature uh to like activate this position because we tried like room temperature. Also, it didn't work. Okay,.

A

um Any other chemistry suggestions, I've got one, but I didn't want to steal anyone's thunder.

C

Torsolate or mesolate, but that would require different rage.

A

I think the the possibility of it being alkylated elsewhere is true, the the pyridine nitrogen I can imagine acting as a little bit of an internal catalyst to make it even worse, because you, you can kind of temporarily look like that, and then you could imagine you transfer a group over to the other, nitrogen or.

C

You can get like some weird intermediate pyridinium.

A

Salt, the other way of doing this alkylation, if you don't want to do to put to put an alkyl group on a nitrogen rather than doing a direct calculation once anyone want to jump in with another possible way of doing that,.

A

It's not an exam just.

A

Asking it's a reductive, amination process: you can you can I'm.

D

Looking I I'm thinking about that, okay, so reductive elimination. We can do like if we put bromine here. Sorry.

A

No on the um on the other slide. Sorry, when you're putting on that the out the alkyl group directly, instead of doing an alkylation, you can use an aldehyde or something and and bring them together and then throwing a reducing agent like sodium borohydride. And so you, you initially from a minimum species, and then you reduce it. That's another possibility.

A

F

I think I brought it up uh to quillin another postdoc in our lab and he told me that most likely was not going to work because it would be too sterically hindered for the reaction to happen.

C

I'm also concerned about that uh book walt hartwig as well, that that could be too sterically hindered because there's.

G

A tert-butyl right.

C

There yeah yes, yes,.

D

So this is the problem why we are getting low yield, but uh yeah we are working on that uh most probably this week we will get something like at least 50 reaction. We can like give.

A

Great well, you know, let's say a week in the lab, saves you an hour in the library, so it's sometimes easier just to go and do it great all right. Good luck.

A

um All right, fantastic, so um I mean from the just. Let me put this back up um so I mean. Obviously that is a an area that we can explore um is. Is you know, continuing to explore the impact of alkalating uh and we've got some nice leads here. I guess my my first question um was to uh add dana and flavia in terms of molecules that are coming through, or that might be the next ones to be coming through or the ones that are obvious to make in response to this.

A

Does anybody want to to nominate you know something or describe something which is coming through and- and I guess I was hoping you could be- uh you know tell us a little bit about what you're doing in the lab. Initially do you want to have some chemistry updates about things that might be relevant to these kinds of structures that are coming through.

E

Yeah, I can just briefly update the the homologous series, so we have the starting material for alkylation, so we have the the the main core with known alkylated compounds so in the molecule series and the an alkylation failed for us using the same method with carboxylation carbonate. So we are trying trying other methods, but uh it's something that should be solved very very soon. So I I think we will have the examples for the homologous room.

E

Okay, yeah, it's not it's not here. Am I on the wrong page. Yeah! Sorry, do you.

A

Happen to have it in front of you or.

E

No, let me see if I can find it here to be easier to just run yeah, so we're sure we're talking about it.

E

I think people can can can go on and and then I I get.

A

Back to you, um george, did you want to have a did? You want to update us on anything or.

H

Yeah I'm trying to synthesize a molecule that is very different. um That means that I don't have I don't I'm I mean I have the core the main core and then attach the imidazole. I have a bending ring and then.

H

Different kind of amines attached to this bending ring, and so basically I am trying to do that. um If you want, I can share the screen if.

A

You got it yeah.

H

I just want to show you what I'm trying to.

H

Do hopefully, you can see that.

G

H

Okay, so I'm trying to attach this uh ring in this position and then uh substitute try to to yeah to put some amines here, um but I have some difficulties in separating uh to purifying this product because it's uh um so the the polarity of the product is quite the same of the certain materials.

H

So I did already two columns but yeah. I I'll try to verify this again.

H

If anyone has some hints I'd appreciate that.

A

This is, this is chromatography right, you're talking about you're, doing by chromatography.

H

I'm doing column chromatography yeah.

A

Yeah and and it's coal is, is there a? Is there a problem with that I mean coeluting or is there it's just? I.

H

Mean that I I for me, it's really difficult to separate them, I mean I'm. I did two columns and okay. The first was not the best one, but the second one was good, and but everything came together. um So what I'm trying to do is maybe trying to do a separation uh with um high ph in this way. Maybe the boronic acid will remain in the aqueous layer um yeah, but doesn't seem really good um yeah.

H

Maybe what I, what I will do is um try to increase the polarity of the column in really really slow way, and maybe in this way I can separate better the different uh spots.

A

Yeah, okay, I thought a world cup from a suzuki involved. A um workout from the suzuki involves an oxidative step. Doesn't it when you do that, so you oxidize the boronic acid to the phenol, and then it comes out more easily. Am I am I out of.

A

A

Experts on the call.

B

I don't know I think at this point we would normally just go for a reverse phase column if you've already done two normal phases and they've not worked.

B

Yeah, I don't know if you've run it on an lcms to see. If it you can see separate peaks.

H

C

Actually, I did only tlc.

H

And and nmr, but the nmr, it's quite messy, so yeah.

A

The idea here is to take this molecule and then substitute the chlorine with an amine. Is that the order here so you're going to get a lot of any divergent synthesis of a bunch of molecules, so you've got to get be able to get this reasonably pure looking on scale right, that's the idea. Okay, all right great! Thank you.

E

So if you, if you don't mind, I can I can share my my screen briefly just to show the compounds that'll be awesome. Okay, uh let me see can't draw.

E

I

E

I think just just one one scheme, all right: okay, so we prepared this one, uh it's okay, so fast, so we have different substitutions here too, not only the methyl group, but also um other other, like the proper methoxy. It's not uh the ideal one but other groups here, and we have this so the alkylation the last step.

E

um It's it's a problem for us now we are not. We are just recovering the starting material, not the uncalculated product, and we we failed doing the alkylation here. So we are. We are changing methods, including the the relative alkylation, using aldehydes for this. So right, let's see if changing the base, we did the same, the same method as larry sent center. So, let's see probably next week or the order will have some updates in your compounds and we will complete our set of two compounds like with five six compounds to send you, okay,.

A

Great okay, all right um and danny, you were doing one part right. Did you want to just do you have anything that summarizes the structures or is it still basically? According to the planet, we had.

J

um Me yeah, I can. It is the same basically as what we discussed, but um so I think it would be on issue whatever it is. I think I've got it. 66 yeah that guy right right right right, um so the.

J

Wow, I'm just blanking all the heterocycle names, but essentially yes, I'm sorry that this is oxazole that one I didn't buy, it's really expensive the um thiazole and the uh the nh. No, no sorry the end methyl.

J

What is that pearl god? What's wrong with me great, I know what it's called anyway. These two reactions, I've done um and they're really they're, just really gross in every way. They smell bad and there's lots of spots, but I'm in the process of purifying them.

C

J

Then I ran out of the isocyanates. I had to order more, but then I'll make the the nh peril as well.

A

Is this microwave.

J

A

um So just with that core, then I mean, I guess, given the data here, wait given the data here which essentially you're modifying what am I doing uh that right so I mean essentially building off this right kind of thing.

J

Yeah, so the the reasoning behind making these is just so that we've thoroughly explored replacements for this two pyral, which we were concerned about toxicity perspective, um so that to fill out the sar. The plan also is to do them on a large enough scale, so that I can take some of the material and then alkylate it and test those compounds as well.

A

Right so I guess the data we just got the most similar compounds of these and what I mean is there is some activity there. So it's not.

C

A

Not a hopeless thing to do right, because if these were inactive and your molecules were inactive, we wouldn't be any wiser. But we have some.

J

Activity here that.

A

We can start with.

J

Right and um so the potentially maybe the the form methyl is more interesting, but that one didn't.

C

J

Isocyanide before fluoro is commercially available, so I just went with that as a one-off, and I think you know we have enough matched pairs with the fourth floor, that we can get some useful data out of it. If any of them look interesting, we can make them with the meth as well.

A

Yeah: okay, okay, that's fine!.

J

Yeah, so that's that's the plan with those yeah.

E

Just a comment for the pyro: this spiral uh formula pyro it's it's very reactive and then not only.

C

E

It by before, exactly not only putting five before using it, but also maybe using a dilute solution of of this while reacting, because this would prevent polymerization and other reactions is reacted. Okay, it's just because our experience previous experience with this chemistry.

E

It's useful to know yeah, you might end.

C

Up with indigo.

A

um Ed, I guess you're done with this yeah, I'm done yeah, because we got nothing, and so I mean from the day. I guess you know we're still tinkering with the right things here, I'm not seeing anything knockout. We need to re-test this we're. Making variants of this flavio is doing the homologation.

C

I think I don't know how hard the analog of 1000 is to make, but if we can take that ring methoxy off uh the the bicyclic methoxy on the bicyclic core, I mean and leave the parody epoxy. That would be very interesting.

C

Are these the ones that came from laurie, I believe so? Yeah.

A

So the question.

J

B

Yeah, all these guys, I think it's just the n-methyl ones.

A

Okay, I mean okay, so I mean a possible question. There is whether or not those exist already if laurie has them. Maybe could that search be done at northeastern.

D

A

D

Have to check it.

A

Yeah yeah yeah, I mean so just around this core. In particular, you know what what what is already known around that maybe without the methoxy, for example, that kind of thing I mean I guess you always want.

C

A

Zoom in on wherever you see the greatest activity.

A

That'd be useful, um any other, I mean any other things we should be doing here. If anyone has any thoughts about what this data is telling them.

D

uh I I have one question: the positive control have like five five uh core. So can we just do like only five, rather than five, six, two five core, only the five member. uh What we call this string!

D

uh We just uh get rid of the six five six ring two. Only five core.

J

Yes, I've made some attempts to do that um and I didn't haven't gotten it to work yet um and then I kind of gave up and didn't come back to it, but I can come back to it and see if I can make it yeah. I think ben suggested trying a negishi coupling um so I can I'll have to. I have to go back and look, but um at what I've tried already but yeah. I did try to make that and I think it would be interesting.

A

And are you suggesting that, because we're kind of getting persistently higher activity with this kind of compound is that is there a reason for the suggestion.

D

Yeah, one of that and the second is, as we are planning to get rid of ome from 100 0001.

D

So it's better to just to remove the ring and see whether it's showing any activity or not.

J

Yeah, well that I mean that is the part, that's getting metabolized right and then I'm. I also wonder if you remove an aromatic ring from like the five six core, if that might help solubility as well, just make it a little bit less flat.

C

Hydrogen I mean how or how would you could probably open up the six? You could probably remove the two double bonds at the end.

J

That's been made the saturated five six, it's been made alvaro made it yeah.

J

So I think that would give you the same issue as the saturated. The five five.

J

But we've never just I've never been able to make just taking off all those methylene carbons. So I I think that could be interesting if we can get the chemistry to work.

A

Yeah, removing this liability, whilst probing that would be really nice, yeah, okay, good, um okay, the other stuff, that's um on the uh su is, can all be done offline. I just wanted to have a conversation about that, so I think that we're getting um cytotoxic from alex pretty soon um the I guess, I'm not sure about whether we uh wait wait, wait. What was I gonna? What was I gonna mention? Sorry, um oh.

J

The commercial amides.

A

Sorry have we ordered those? I can't remember.

J

Yes and the lead time is about a month. um I checked in a couple weeks ago, so um I'll I'll, keep we'll follow I'll, keep following up on that and just kind of making sure that it's happening okay. But it's it's expected to take a while. So.

A

So yeah, okay, great, um that's fine! I'm also in touch with lee about the mechanism reaction experiment, so I'll keep pursuing that um uh northeastern friends. If you were able to get github accounts, we could talk on here. If that's possible, just log in sign in get an account, then we can ping you if we need things I think of the people on this meeting you're the only guys without accounts right unless you, unless you got them.

A

So if you were able to if you're able to get accounts, we could correspond here.

A

It's a pretty it's a pretty! Please.

A

Okay, oh good. Anyone else want to raise anything while we're all here. I think everything else can wait till next time.

A

All right, in that case, thank you very much for coming nice to see everybody. Thank you see you next time bye. I think.