About this Author
Derek Lowe, an Arkansan by birth, got his BA from Hendrix College and his PhD in organic chemistry from Duke before spending time in Germany on a Humboldt Fellowship on his post-doc. He's worked for several major pharmaceutical companies since 1989 on drug discovery projects against schizophrenia, Alzheimer's, diabetes, osteoporosis and other diseases.
To contact Derek email him directly: email@example.com
November 2, 2012
That title should bring in the hits. But don't get your hopes up! This is medicinal chemistry, after all.
"Can't you just put the group in your molecule that does such-and-such?" Medicinal chemists sometimes hear variations of that question from people outside of chemistry - hopeful sorts who believe that we might have some effective and instantly applicable techniques for fixing selectivity, brain penetration, toxicity, and all those other properties we're always trying to align.
Mostly, though, we just have general guidelines - not so big, not so greasy (maybe not so polar, either, depending on what you're after), and avoid a few of the weirder functional groups. After that, it's art and science and hard work. A recent J. Med. Chem. paper illustrates just that point - the authors are looking at the phenomenon of molecular promiscuity. That shows up sometimes when one compound is reasonably selective, but a seemingly closely related one hits several other targets. Is there any way to predict this sort of thing?
"Probably not", is the answer. The authors looked at a range of matched molecular pairs (MMPs), structures that were mostly identical but varied only in one region. Their data set is list of compounds in this paper from the Broad Institute, which I blogged about here. There are over 15,000 compounds from three sources - vendors, natural product collections, and Schreiber-style diversity-oriented synthesis. The MMPs are things like chloro-for-methoxy on an aryl ring, or thiophene-for-pyridyl with other substituents the same. That is, they're just the sort of combinations that show up when medicinal chemists work out a series of analogs.
The Broad data set yielded 30954 matched pairs, involving over 8000 compounds and over seven thousand different transformations. Comparing these compounds and their reported selectivity over 100 different targets (also in the original paper), showed that most of these behaved "normally" - over half of them were active against the same targets that their partners were active against. But at the other end of the scale, 829 compounds showed different activity over at least ten targets, and 126 of those compounds different in activity by fifty targets or more. 33 of them differed by over ninety targets! So there really are some sudden changes out there waiting to be tripped over; they're not frequent, but they're dramatic.
How about correlations between these "promiscuity cliff" compounds and physical properties, such as molecular weight, logP, donor/acceptor count, and so on? I'd have guessed that a change to higher logP would have accompanied this sort of thing over a broad data set, but the matched pairs don't really show that (nor a shift in molecular weight). On the other hand, most of the highly promiscuous compounds are in the high cLogP range, which is reassuring from the standpoint of Received Med-Chem Wisdom. There are still plenty of selective high-logP compounds, but the ones that hit dozens of targets are almost invariably logP > 6.
Structurally, though, no particular substructure (or transformation of substructures) was found to be associated with sudden onset of promiscuity, so to this approximation, there's no actionable "avoid sticking this thing on" rule to be drawn. (Note that this does not, to me at least, say that there are no such things are frequent-hitting structures - we're talking about changes within some larger structure, not the hits you'd get when screening 500 small rhodanine phenols or the like). In fact, I don't think the Broad data set even included many functional groups of that sort to start with.
On the basis of the data available to us, it is not possible to conclude with certainty to what extent highly promiscuous compounds engage in specific and/or nonspecific interactions with targets. It is of course unlikely that a compound might form specific interactions with 90 or more diverse targets, even if the interactions were clearly detectable under the given experimental conditions. . .
. . .it has remained largely unclear from a medicinal chemistry perspective thus far whether certain molecular frameworks carry an intrinsic likelihood of promiscuity and/or might have frequent hitter character. After all, promiscuity is determined for compounds, not their frameworks. Importantly, the findings presented herein do not promote a framework-centric view of promiscuity. Thus, for the evaluation and prioritization of compound series for medicinal chemistry, frameworks should not primarily be considered as an intrinsic source of promiscuity and potential lack of compound specificity. Rather, we demonstrate that small chemical modifications can trigger large-magnitude promiscuity effects. Importantly, these effects depend on the specific structural environment in which these modifications occur. On the basis of our analysis, substitutions that induce promiscuity in any structural environment were not identified. Thus, in medicinal chemistry, it is important to evaluate promiscuity for individual compounds in series that are preferred from an SAR perspective; observed specificity of certain analogs within a series does not guarantee that others are not highly promiscuous."
Point taken. I continue to think, though, that some structures should trigger those evaluations with more urgency than others, although it's important never to take anything for granted with molecules you really care about.
+ TrackBacks (0) | Category: Chemical News | Drug Assays | Natural Products | Toxicology
August 26, 2011
We're going to need new antibiotics. Everyone knows this, and it's not like no one's been trying to do anything about it, either, but. . .we're still going to need more of them than we have. I'm not predicting that we're going to go all the way back to a world where young, healthy people with access to the best medical care die because they decided to play tennis without their socks on, but we're certainly in danger of a much nastier world than we have.
So I'm always interested to hear of new antibiotic discovery programs, and Merck is out with an interesting paper on theirs. They've been digging through the natural products, which have been the fount from which almost all antibiotics have sprung, and they have a new one called kibdelomycin to report. This one was dug out from an organism in a sample from the Central African Republic by a complicated but useful screening protocol, the S. aureus fitness test. This relies on 245 different engineered strains of the bacterium, each with an inducible RNAi pathway to downregulate some essential gene. When you pool these into mixed groups and grow them in the presence of test compounds (or natural product extracts) for 20 generations or so, a check of what strains have moved ahead (and fallen behind) can tell you what pathways you seem to be targeting. A key feature is that you can compare the profile you get with those of known antibiotics, so you don't end up rediscovering something (or discovering something that only duplicates what we already have anyway).
Now, that's no one's idea of a beautiful structure, although (to be fair) a lot of antibiotics have very weird structures themselves. But it's safe to say that there are some features there that could be trouble in a whole animal, such as that central keto-enol-pyrrolidone ring and the funky unsaturated system next to it. (The dichloropyrrole, though, is interestingly reminiscent of these AstraZeneca gyrase/topoisomerase antibiotic candidates, while both celestramycin and pyoluteorin have a different dichloropyrrole in them).
What kind of activity does kibdelomycin have? Well, this is where my enthusiasm cools off just a bit more. It showed up in screening with a profile similar to the coumarin antibiotics novobiocin and chlorobiocin, and sure enough, it's a topoisomerase II inhibitor. It appears to be active almost entirely on gram-positive organisms. And while there are certainly nasty gram-positive infections that have to be dealt with, I'm more encouraged when I see something that hits gram-negatives as well. They've got more complicated defenses, those guys, and they're harder to kill. It's not easy to get broad-spectrum activity when you're going after gyrase/Topo II, but the fluoroquinolones definitely manage it.
The Merck team makes much out of kibdelomycin being "the first truly novel bacterial type II topoisomerase inhibitor with potent antibacterial activity discovered from natural product sources in more than six decades". And they're right that this is an accomplishment. But the kicker in that sentence is "from natural product sources". Getting gram-positive Topo II inhibitors has actually been one of the areas where synthetic compounds have had the most success. Building off the quinolones themselves has been a reasonably fruitful strategy, and a look through the literature turns up a number of other structural classes with this sort of activity (including some pretty wild ones). Not all of these are going places, but there are certainly a number of possibilities out there.
In short, if kibdelomycin weren't an odd-looking natural product, I wonder how much attention another high-molecular-weight gram-positive-only topoisomerase inhibitor would be getting, especially with only in vitro data behind it. Every little bit helps, and having a new structural class to work from is a worthwhile discovery. But one could still want (and hope) for more.
+ TrackBacks (0) | Category: Drug Assays | Infectious Diseases | Natural Products
December 15, 2010
Thanks to an email from a reader, I can bring you this very weird paper from Tetrahedron. The authors claim to have extracted a local plant and isolated nevirapine, (sold as Viramune by Boehringer Ingleheim as a reverse transcriptase inhibitor for HIV).
That's kind of odd. I'm no natural products expert, but I've sure seen a lot of them over the years, and that framework (and the N-cyclopropyl) don't look so likely to me. But hey, plants do odd things. That's not what's really puzzling about this paper. No, what's had me staring at it this morning is the claim that, in contrast to the marketed drug, this stuff is optically active nevirapine.
Say what? Try as I might, I can't see any plausible way that that's a chiral compound. The authors seem to think it is, though. They claim optical rotation, somehow, and then say that "The detailed structure and stereochemistry of compound 1 was established unambiguously by single crystal X-ray crystallography." But hold on - that's not as easy as it sounds. Getting absolute configurations from the X-ray data of light-atom-only molecules takes special efforts, and I don't see any being taken (molybdenum X-rays, direct methods, no talk of anomalous dispersion, etc.)
I'm just not willing to see that nitrogen atom as a source of chirality - if it were, shouldn't that be the focus of this whole paper? Instead, the authors just blithely tell us how neat it is that they've isolated the chiral material. In fact, they find it so neat that they tell us two times in a row:
This is a very interesting discovery that naturally occurring optically active nevirapine has been biosynthesized in the seeds of C.viscosa and the optically inactive nevirapine was designed as a selective non-nucleoside inhibitor of HIV-1 reverse transcriptase. It is also a remarkable ﬁnding that the seed of C.viscosa is the source of optically active nevirapine, which was also designed and synthesized before its isolation from natural source.
This sounds like some sort of lunatic patent-busting exercise, to be honest. And it sounds as if someone doesn't know what a chiral compound is. And that whoever reviewed this for Tetrahedron was incompetent. And that the editor who let it through should be a least a little bit ashamed. Well?
+ TrackBacks (0) | Category: Infectious Diseases | Natural Products | The Scientific Literature
November 11, 2010
I've been reading an interesting new paper from Stuart Schreiber's research group(s) in PNAS. But I'm not sure if the authors and I would agree on the reasons that it's interesting.
This is another in the series that Schreiber has been writing on high-throughput screening and diversity-oriented synthesis (DOS). As mentioned here before, I have trouble getting my head around the whole DOS concept, so perhaps that's the root of my problems with this latest paper. In many ways, it's a companion to one that was published earlier this year in JACS. In that paper, he made the case that natural products aren't quite the right fit for drug screening, which fit with an earlier paper that made a similar claim for small-molecule collections. Natural products, the JACS paper said, were too optimized by evolution to hit targets that we don't want, while small molecules are too simple to hit a lot of the targets that we do. Now comes the latest pitch.
In this PNAS paper, Schreiber's crew takes three compound collections: 6,152 small commercial molecules, 2,477 natural products, and 6,623 from academic synthetic chemistry (with a preponderance of DOS compounds), for a total of 15, 252. They run all of these past a set of 100 proteins using their small-molecule microarray screening method, and look for trends in coverage and specificity. What they found, after getting rid of various artifacts, was that about 3400 compounds hit at least one protein (and if you're screening 100 proteins, that's a perfectly reasonable result). But, naturally, these hits weren't distributed evenly among the three compound collections. 26% of the academic compounds were hits, and 23% of the commercial set, but only 13% of the natural products.
Looking at specificity, it appears that the commercial compounds were more likely, when they hit, to hit six or more different proteins in the set, and the natural products the least. Looking at it in terms of compounds that hit only one or two targets gave a similar distribution - in each case, the DOS compounds were intermediate, and that turns out to be a theme of the whole paper. They analyzed the three compound collections for structural features, specifically their stereochemical complexity (chiral carbons as a per cent of all carbons) and shape complexity (sp3 carbons as a percent of the whole). And that showed that the commercial set was biased towards the flat, achiral side of things, while the natural products were the other way around, tilted toward the complex, multiple-chiral-center end. The DOS-centric screening set was right in the middle.
The take-home, then, is similar to the other papers mentioned above: small molecule collections are inadequate, natural product collections are inadequate: therefore, you need diversity-oriented synthesis compounds, which are just right. I'll let Schreiber sum up his own case:
. . .Both protein-binding frequencies and selectivities are increased among compounds having: (i) increased content of sp3-hybridized atoms relative to commercial compounds, and (ii) intermediate frequency of stereogenic elements relative to commercial (low frequency) and natural (high frequency) compounds. Encouragingly, these favorable structural features are increasingly accessible using modern advances in the methods of organic synthesis and commonly targeted by academic organic chemists as judged by the compounds used in this study that were contributed by members of this community. On the other hand, these features are notably deficient in members of compound collections currently widely used in probe- and drug-discovery efforts.
But something struck me while reading all this. The two metrics used to characterize these compound collections are fine, but they're also two that would be expected to distinguish them thoroughly - after all, natural products do indeed have a lot of chiral carbons, and run-of-the-mill commercial screening sets do indeed have a lot of aryl rings in them. There were several other properties that weren't mentioned at all, so I downloaded the compound set from the paper's supporting information and ran it through some in-house software that we use to break down such things.
I can't imagine, for example, evaluating a compound collection without taking a look at the molecular weights. Here's that graph - the X axis is the compound number, Y-axis is weight in Daltons:
The three different collections show up very well this way, too. The commercial compounds (almost every one under 500 MW) are on the left. Then you have that break of natural products in the middle, with some real whoppers. And after that, you have the various DOS libraries, which were apparently entered in batches, which makes things convenient.
Notice, for example that block of them standing up around 15,000 - that turns out to be the compounds from this 2004 Schreiber paper, which are a bunch of gigantic spirooxindole derivatives. In this paper, they found that this particular set was an outlier in the academic collection, with a lot more binding promiscuity than the rest of the set (and they went so far as to analyze the set with and without it included). The earlier paper, though, makes the case for these compounds as new probes of cellular pathways, but if they hit across so many proteins at the same time, you have to wonder how such assays can be interpreted. The experiments behind these two papers seem to have been run in the wrong order.
Note, also, that the commercial set includes a lot of small compounds, even many below 250 MW. This is down in the fragment screening range, for sure, and the whole point of looking at compounds of that molecular weight is that you'll always find something that binds to some degree. Downgrading the commercial set for promiscuous binding when you set the cutoffs that low isn't a fair complaint, especially when you consider that the DOS compounds have a much lower proportion of compounds in that range. Run a commercial/natural product/DOS comparison controlled for molecular weight, and we can talk.
I also can't imagine looking over a collection and not checking logP, but that's not in the paper, either. But here you are:
In this case, the natural products (around compound ID 7500) are much less obvious, but you can certainly see the different chemical classes standing out in the DOS set. Note, though, that those compounds explore high-logP regions that the other sets don't really touch.
How about polar surface area? Now the natural products really show their true character - looking over the structures, that's because there are an awful lot of polysaccharide-containing things in there, which will run your PSA up faster than anything:
And again, you can see the different libraries in the DOS set very clearly.
So there are a lot of other ways to distinguish these compounds, ways that (to be frank) are probably much more relevant to their biological activity. Just the molecular-weight one is a deal-breaker for me, I'm afraid. And that's before I start looking at the structures in the three collections at all. Now, that's another story.
I have to say, from my own biased viewpoint, I wouldn't pay money for any of the three collections. The natural product one, as mentioned, goes too high in molecular weight and is too polar for my tastes. I'd consider it for antibiotic drug discovery, but with gritted teeth. The commercial set can't make up its mind if it's a fragment collection or not. There are a bunch of compounds that are too small even for my tastes in fragments - 4-methylpyridine, for example. And there are a lot of ugly functional groups: imines of beta-napthylamine, which should not even get near the front door (unstable fluorescent compounds that break down to a known carcinogen? Return to sender). There are hydroxylamines, peroxides, thioureas, all kinds of things that I would just rather not spend my time on.
And what of the DOS collection? Well, to be fair, not all of it is DOS - there are a few compounds in there that I can't figure out, like isoquinoline, which you can buy from the catalog. But the great majority are indeed diversity-oriented, and (to my mind), diversity-oriented to a fault. The spirooxindole library is probably the worst - you should see the number of aryl rings decorating some of those things; it's like a fever dream - but they're not the only offenders in the "Let's just hang as many big things as we can off this sucker" category. Now, there are some interesting and reasonable DOS compounds in there, too, but there are also more endoperoxides and such. (And yes, I know that there are drug structures with endoperoxides in them, but damned few of them, and art is long while life is short). So no, I wouldn't have bought this set for screening, either; I'd have cherry-picked about 15 or 20% of it.
Summary of this long-winded post? I hate to say it, but I think this paper has its thumb on the scale. I'm just around the corner from the Broad Institute, though, so maybe a rock will come through my window this afternoon. . .
+ TrackBacks (0) | Category: Academia (vs. Industry) | Drug Assays | Drug Development | Natural Products
August 26, 2010
The Vinca alkaloids are some of the most famous chemotherapy drugs around - vincristine and vinblastine, the two most widely used, are probably shown in every single introduction to natural products chemistry that's been written in the past fifty years. But making them synthetically is a bear, and extracting them from the plant is a low-yielding pain.
A new paper in PNAS shows that there's still a lot that we don't know about these compounds. What has been known for a long time is that they're derived from two precursor alkaloids, vindoline and catharanthine. This new work shows that the plants deliberately keep those two compounds separated from each other, which helps account for the low yield of the final compounds.
As it turns out, if you dip the leaves in chloroform, which dissolves the waxy coating from the surface, you find that basically all the catharanthine is found there. At the same time, even soaking the leaves in chloroform for as long as an hour hardly extracts any vindoline - it's sequestered away inside the cells of the leaves. The enzymes responsible for biosynthesis are probably also in different locations (or cell types), and there are unknown transport mechanisms involved as well. This is the first time anyone's found such a secreted alkaloid mechanism.
Why does Vinca go to all the trouble? For one thing, catharanthine is a defense against insect pests, and it also seems to inhibit attack by fungal spores. And what the vindoline is doing, I'm not sure - but the plant probably has a good reason to keep it away from the cantharanthine, because producing too much vincristine, vinblastine, etc. would probably kill off its dividing cells, the same way it works in chemotherapy.
The authors suggest that people should start looking around to see if other plants have similar secretion mechanisms. And this makes me wonder if this could be a way to harvest natural products - do the plants survive after having their leaves dipped in solvent? If they do, do they then re-secrete more natural waxes to catch up? I'm imagining a line of plants, growing in pots on some sort of conveyor line, flipping upside down for a quick wash-and-shake through a trough of chloroform, and heading back into the greenhouse. . .but then, I have a vivid imagination. . .
+ TrackBacks (0) | Category: Biological News | Natural Products