How much do we really know about what small drug molecules do when they get into cells? Everyone involved in this sort of research wonders about this question, especially when it comes to toxicology. There's a new paper out in PLoS One that will cause you to think even harder.

The researchers (from Princeton) looked at the effects of the antidepressant sertraline, a serotonin reuptake inhibitor. They did a careful study in yeast cells on its effects, and that may have some of you raising your eyebrows already. That's because yeast doesn't even have a serotonin transporter. In a perfect pharmacological world, sertraline would do nothing at all in this system.

We don't live in that world. The group found that the drug does enter yeast cells, mostly by diffusion, with a bit of acceleration due to proton motive force and some reverse transport by efflux pumps. (This is worth considering in light of those discussions we were having here the other day about transport into cells). At equilibrium, most (85 to 90%) of the sertaline that makes it into a yeast cell is stuck to various membranes, mostly ones involved in vesicle formation, either through electrostatic forces or buried in the lipid bilayer. It's not setting off any receptors - there aren't any - so what happens when it's just hanging around in there?

More than you'd think, apparently. There's enough drug in there to make some of the membranes curve abnormally, which triggers a local autophagic response. (The paper has electron micrographs of funny-looking Golgi membranes and other organelles). This apparently accounts for the odd fact, noticed several years ago, that some serotonin reuptake inhibitors have antifungal activity. This probably applies to the whole class of cationic amphiphilic/amphipathic drug structures.

The big question is what happens in mammalian cells at normal doses of such compounds. These may well not be enough to cause membrane trouble, but there's already evidence to the contrary. A second big question is: does this effect account for some of the actual neurological effects of these drugs? And a third one is, how many other compounds are doing something similar? The more you look, the more you find. . .

This fine reagent was mentioned here (disparagingly) in the comments the other day, and I knew that it was time to add it to the list. I've had some other selenium entries before, and they're all here for the same reason: their unsupportable stenches. Everyone, even people who've never had a chemistry class in their lives, knows that sulfur compounds are stinky, of course, but it's a problem that continues as you move down Group XVI of the periodic table.

And it's not like plain phenol itself has no odor. It's strong, penetrating, and completely unmistakable. As soon as I get a whiff of the stuff, I'm immediately transported back to the Verser Clinic, the small hospital in the town I grew up in back in Arkansas. Phenol smells like an old-fashioned medical office; it was used for many years as a disinfectant (and was, in fact, introduced as such by Joseph Lister himself). If you move it down a notch to sulfur, you get thiophenol, which is easy to describe: burning rubber - the pure, potent, platonic ideal of burning rubber, bottled up and daring you to open the cap. I can't say that I won't work with thiophenol, since I have (very much to my regret, at times), but I've used it most reluctantly, and probably haven't touched it in at least fifteen years.

Ah, but move down one more element and you have selenophenol, and that's a more exotic reagent. I've never seen any, and after reading the descriptions, I never want to. Actually, let me take that back: I'd look at some from the other end of the lab. What I never want to do is open any of it up. The chemical literature has numerous examples of people who are at a loss for words when it comes to describing its smell, but their attempts are eloquent all the same. A few years ago, Gaussling at the Lamentations on Chemistry blog referred to it as "The biggest stinker I have run across. . .Imagine 6 skunks wrapped in rubber innertubes and the whole thing is set ablaze. That might approach the metaphysical stench of this material." So we'll start with that.

I believe that this lovely compound is commercially available (if you're anywhere close to anyone making it, you'll know about it). But should you wish to prepare it with your own hands, do violence to your own schnozz, and drape yourself out of your own window while you throw up into your own rhododendrons, feel free to use this reliable preparation from Organic Syntheses, circa 1944. This features the note that "it is frequently advisable to work with [selenium compounds] on alternate days", which I suppose is to give them time to work their way out of your nasal passages.

I'm not so sure. When I was a teaching assistant in grad school, I taught three labs a week one semester, and one of those labs, damn it all, was the phenyl Grignard reagent. We had them making it in diethyl ether, outside of the small and inadequate fume hoods, and the solvent fumes were fit to strip paint. By the end of the Monday lab, I was well saturated with ether and had a terrible headache, which returned as soon as I caught my first whiff of the stuff on Tuesday afternoon. I barely made it through that lab, mostly by holding my breath and using a lot of hand gestures, and I took the opportunity on Wednesday to get as much fresh air as I could. But when I came back for the Thursday session, the first first wave of ether vapor washed over me and nearly stretched me out on the tiles. I taught the entire lab from the hallway, shouting and waving like Monty Python's "Semaphore Version of Wuthering Heights". So in my mind, the choice between getting these things over with and stretching them out is still not settled.

That Org Syn prep also notes that it can produce small amounts of hydrogen selenide, which is very toxic indeed (and will give you a sore throat, too, apparently, before it kills you). This luckless graduate student from the 1920s got to experience both of these bracing selenium room fresheners in the course of his work:

Berzelius described the poisonous effect of hydrogen selenide quite impressively; "In order ta get acquainted with the smell of this gas I allowed a bubble not larger than a pea to pass into my nostril ; in consequence of its smell I so completely loss my sense of smell for several hours that I could not distinguish the odor of strong ammonia even when held under my nose. My sense of smell returned after five or six hours, but severe irritation of the mucous membrane set in and persisted for a fortnight' The writer has been working on the gas for some time and was also quite seriously affected once, the injury persisting for many days. That it is more poisonous than the hydrogen sulphide is well known."

So you have that to look forward to on your way to selenophenol. And at your destination? Assuming your nose is still attached to your face, you'll experience what few chemists ever have. I'll let this 1908 report from Wisconsin take over:

When benzeneselenonic acid in solution is treated with reducing agents such as hydrogen sulphide, sulphur dioxide, or, best, with zinc and hydrochloric, acid selenophenol is obtained as a yellow oil with an overpowering and most nauseating odor. . .The odor of diphenyl diselenide is extremely disagreeable but is not nearly so bad as that of selenophenol.

. . .The effect of selenophenol on the skin is very similar to that of thiophenol, forming blisters which itch intensely. After a time, these dry up, the skin scales off, and there appears to be a deposit of red selenium beneath it. The odor of selenophenol is very penetrating, and is nauseating beyond description.

Gloves, man, gloves. Unless, of course, you wish to be tattooed with elemental selenium while being nauseated beyond description. Should this be your idea of a fun Saturday night, I will not stand in your way.

Now here's a worrisome thought, if you're doing kinase research. A tyrosine kinase inhibitor in the clinic against Bcr-Abl, bosutinib (SKI-606), is also being used as a research tool in a number of academic groups. But they're probably not using what they think they're using.

This article has the details. The compound has a dichloromethoxy aryl group hanging off of it, and apparently someone has been making (or made one good-sized batch of) the wrong isomer. Instead of 2, 4-dichloro-5-methoxy, many commercial samples appear to be 3,5-dichloro-4-methoxy. This got noticed at first by inspection of an X-ray structure deposited in the Protein Data Bank, 3ZZ2, from a group at Oxford. A postdoc at Stanford saw that something was off, and at the same time, he was having trouble matching his own X-ray data with the known structure of the compound.

The explanation wasn't what anyone wanted to hear, for sure. The two groups had purchased their material years apart, from different vendors. The count of vendors selling the wrong material is now up to thirteen and climbing. That link also suggests a possible earlier source of the problem: some of the commercial supplies of 2,4-dichloro-5-methoxy aniline are not the right material. Whoever made this bosutinib may well have thought that they were right on target.

Odds are, some batch of the wrong stuff has been resold through the supplier community since at least 2006 - this sort of thing goes on all the time. But the tricky part here is that LC/MS wouldn't have told you that there was a problem, unless you had an authentic sample to check the retention times (which would have been pretty darn close, anyway, I'd guess). The mass is, of course, the same. And the NMRs of the authentic and mis-labeled stuff would be different, but not on casual inspection, for sure (same number of aryl protons). No, I would have let this stuff through, I've no doubt about that. Makes a person wonder what else on the shelf is the wrong material, doesn't it?

A reader sends along this query, which I thought asked a very useful question:

". . .as a member of a growing biopharma company I am tasked with evaluating the effectiveness of industrial post-docs from both a business perspective and the post-doc's experience. Specifically, we are considering adding one for a short-term (2yr) to add headcount to a project. This adds resources without the long term commitment and also gives the scientists on site a chance for a paper they otherwise might not have time to work on. The candidate obviously gets a well-paid post-doc experience, and an industrial foot in the door. But, does this model work? I imagine that if it were that cut and dried you would see more of them."

Good point. Industrial post-docs are still relatively rare, although I've certainly seen a few. Come to think of it, though, those were mostly in biology, as opposed to chemistry. So, what do people think? From my end, I'd say that traditionally, companies have felt that temporary positions are best filled with experienced temporary employees, who presumably don't have to be trained as much. And if you're going to hire someone to learn the ropes, they might as well be good enough to be brought in as a full-time employee.

From the other end, an industrial post-doc has always been seen as less prestigious than an academic one, and there are some hiring managers who probably don't know what to think when one shows up on a c.v. There's often a feeling that if the person did a really good job during the post-doc that the company would have tried to offer them something permanent. And since they didn't, well. . .

Even so, it does seem as if there are situations where an industrial post-doc could be a good fit, and in today's job market, anything looks good. Anyone out there experienced this, from either end?

You chemists may have really stretched things to get a reaction to work, but here's a good set of "Conditions You'll Probably Never Be Desperate Enough to Try". Bone meal? Ground carrots? I think he has a point.

Drug companies are very attuned to competitive intelligence. There's a lot of information sloshing around out there, and you'd be wise to pay attention to it. Publications in journals are probably the least of it - by the time something written up for publication from inside a pharma company, it's either about to be on the drugstore shelves or it never will be at all. Patents are far more essential, and if you're going to watch anything, you should watch the patent applications in your field.

But there's more. Meetings are a big source of disclosure, as witness the Wall Street frenzies around ASCO and the like. Talks and posters release information that won't show up in the literature for a long time (if indeed it ever does). And there are plenty of other avenues. The question is, though, how much time and money do you want to spend on this sort of thing?

There are commercial services (such as Integrity) that monitor companies, compounds, and therapeutic areas in this fashion, and they're happy to sell you their services, which are not cheap. But figuring out the cost/benefit ratio isn't easy. My guess is that these things, while useful, can be thought of as insurance. You're paying to make sure that something big doesn't happen that you're unware or (or unaware of in enough time).

So here's a question for the readership: has competitive intelligence ever made a big difference for you? Positive and negative results both welcome; "I'm so glad we found out about X" versus "I really wish we'd known about Y". Any thoughts?

Here's an excellent article, with copious references, tracing the history of what we now know as the metal-catalyzed coupling field. Victor Snieckus of Queen's University, Thomas Colacot (Johnson Matthey) and co-authors go back to the Wurtz and Glaser reactions of the 1850s and 60s, up through the Ullmann reaction (1891, and still very much with us) and Kharasch and Cadiot-Chodkiewicz couplings (1940s) before breaking into the world of palladium with the Wacker oxidation.

Along the way, one learns that the discoverer of palladium (Wollaston) could never interest anyone in the metal, and almost all of it that he'd extracted was still sitting on the shelf, unsold, at his death. Time vindicated him, and how - it's now perhaps the most essential catalytic metal in the world. The late 1960s were a turning point:

Entry of Richard Heck: Following post-doctoral studies, Heck accepted a position at Hercules Powder Co where he was afforded freedom that is seldom experienced by the modern industrial chemist. Briefed with the task of “doing something with transition metals,” Heck investigated the chemistry of cobalt carbonyl complexes. Although this work generated many interesting observations, finding profitable applications for his research proved difficult. Inspired by his colleague Pat Henry's work on the Wacker oxidation, Heck's attention turned in the direction of arylpalladium chemistry.

He tried Wacker-type conditions with other reagents around to try to intercept the palladium intermediate, and organomercurys obliged with an immediate reaction. The story from there is a trip through a good swath of the periodic table, and the development of an awful lot of knowledge and expertise in metal complexes. Enter then Mizoroki, Kumada, Sonogashira, Negishi, Stille, Suzuki and many others. It's a long, complex, story, but this paper should serve as the definitive overview, and an excellent look at how chemistry (and science in general) go about discovering and developing things.

For those of you following Arena Pharmaceuticals and their long-running efforts to get lorcaserin approved by the FDA, there's a committee hearing on that matter today. Adam Feuerstein is live-blogging the event here. The big issues, now with fresh data: tumors in rat models, and possible heart-valve damage, versus efficacy. The FDA has until June 27 to make a decision.

More disruption in the scientific publishing model: the UK government has announced that it will set up an open-access system for papers that are generated through its funding, similar to the system in the US. The details are still being worked out, and the government is still making noises about not "ruining the value provided by academic publishers", but it's that value that's at issue, isn't it?

A statement from Wiley said that "Publishers enable content digitisation, rigorous peer review, strong editorial infrastructure and support and investment in an effective online platform for dissemination." And yes, they do those things. But how well do they do them? And how well do they do them for the prices they charge? I'm glad that these arguments are finally out on the table.

I mentioned the other day that Human Genome Sciences had turned down an offer from GSK, feeling that they could do better. Well, if they can, now's the time: GSK is now offering the same deal ($13/share) on the open market in a hostile takeover attempt. One of these companies is wrong about that price, and now I guess we'll find out which one of them it is. . .

I've received another e-mail from Prof. Fathi Moussa, lead author of the C60 longevity paper that's been discussed around here. I'd sent a list of the critiques that had shown up in the comments sections, and here's the reply:

An erratum with the right figures 3 and 4 will be published soon in Biomaterials. The right lifespan values after the beginning of the treatment are given in the original text without any change. To sum it up, the extensions of lifespans are twenty months and sixteen months with respect to water-treated controls and olive-oil-treated controls, respectively.

Our original objective was not to study lifespan extension but the toxic effects of C60 at reiterated doses. Lifespan extension by C60 is not really surprising, all the more so as it had already been shown by others that some C60-derivatives can prolong lifespans in several experimental models, albeit moderately.

What is really surprising in our results is that C60 acts at very low doses, which means that the effect is very strong, and that this effect lasts for a long time after the end of the administration. A possible explanation is that some C60 precipitated inside the reticulo-endothelial system and then slowly dissolves and diffuses.

Of course we understand that non C60 specialist readers are incredulous about these results, as it could be expected.

We hope now that others will try and confirm our results. If our results are confirmed by others, which we firmly believe, it will be then necessary to try to reproduce these experiments on bigger samples including other species and of course to optimize the dose and the duration of the treatment.

I share that hope that others will try to confirm the results. It'll be a while, most likely, before we hear about anything in this area, but when something comes up, I'll blog about it.

I've written here before about reaction discovery schemes, and the reaction to those reactions has been, well, mixed. I like them, some other people like them, but some other people are quite offended by the "random search" mentality behind these ideas.

Well, prepare yourselves for another technology for exploring the wild blue yonder. A new paper in Angewandte Chemie from a group at the CEA (Gif sur Yvette, France) outlines an immunological detection scheme. They have antibodies to an imidazole derivative, and antibodies to a phenolic moeity as well. So both structures are attached to a range of functional groups and combined with heat and/or metal catalysts to see if anything happens. A sandwich assay at the end with the different antibodies gives you a yellow color only if a compound has been formed that has both ends present; that is, if a coupling reaction of some sort has occurred.

They ran 3360 reactions, each on a 100 nmol scale (there's the sensitivity of the antibodies for you). Two new reactions were discovered - an isourea synthesis (which can lead to benzoxazoles) and an alkyne reaction leading to thiazole derivatives. Neither of those is going to set the world of organic chemistry ablaze, but as a proof of concept, I'm convinced that this technique can work. So what do you do with it next?

One plan looks to be discovering new bioorthogonal reactions, couplings that can take place either inside or on the surface of living cells. The immunological detection is so sensitive that products can be teased out of all sorts of messy mixtures, apparently even cell lysates. I'd also encourage them to try some other conditions, such as various photochemical setups, to see what might be out there - it's a much less explored field than copper-catalyzed coupling reactions.

Like it or not, I think we're going to be seeing more of this sort of work. We might as well make the most of it!

A number of people have sent me this article about the number of people with Master's and PhD degrees who are receiving food stamps. And while it's undeniable that the numbers have grown, I'd ask for everyone to keep their statistical glasses on. According to the chart at the end of the piece, the percentage of doctorate holders receiving assistance went from 0.05% in 2007 to 0.15% in 2010. (For MS/MA degree holders, it went from 0.5% to 1.3% over that same time).

So it can't be said that this is a widespread phenomenon. One would also want to see the numbers broken down by age cohort, and (especially) by field of study. The examples in the article are all history and English types. Also, if those figures are correct, the headline could have just as easily read "Master's Degree Holders Ten Times More Likely To Be On Food Stamps".

Honestly, the number I find most alarming in that chart is the total number of advanced degree holders. We went from 20 million in 2007 to 22 million in 2010 - two million more in only three years? The population of the country went from 301 million to 313 million during that time, so that's a pretty good crop of degree holders. Given what the economy has been like during that period, I'm surprised the food stamp figures aren't even higher.

Looking at advanced degrees as a percentage of the population, we have 4.3% in 1970, 7.2% in 1980, 8.8% in 1990, 8.6% in 2000 (a decrease I'm at a loss to explain), and 10.6% in 2009. Those figures don't quite add up with the ones in the food stamp article, but the trend certainly is in the same direction. We have figures in the growth in bachelor's degree or higher going back to 1940, and they show the relentless uptrend you'd expect.

So it shouldn't come as a surprise that well-educated people are participating more in some of the downsides that hit the rest of the population. Well-educated people are becoming more and more of the population.

You'll remember the Sanofi chemist who was caught selling proprietary compounds through her own Chinese outsourcing company. Now, via Pharmalot, comes word that Yuan Li has been sentenced to 18 months in prison, along with paying $131,000 in restitution. This foolproof business plan has turned out not to perform up to expectations. Perhaps this example will keep another fool from trying it?

I've received a reply from Dr. Fathi Moussa at Université Paris-Sud, lead author of the C60 longevity paper that I blogged about here, which turned out to have a duplicated figure. With permission, here are the main points of the e-mail:

Of course, you are right: in the published figure 4 the GAog and GAip panels are identical. These two panels were meant to represent the well-known effect of intra-peritoneally (i.p.) administered CCl4 on rat livers. The mistake was obviously due to the fact that the pretreatment of control animals with water either orally (GAog) or i.p. (GAip) cannot influence the effects of CCl4 on livers. Therefore the effects on liver are identical and the corresponding figures are expected to be closely alike. Anyway we sent to the Editor an erratum that will be published soon.

We are very grateful to you for warning us about this figure. We are very furious against ourselves. We still do not understand how such error could have escaped our notice during the revision process. While this mistake has not any influence on the validity of the results described in the text, this could raise a certain amount of doubt over the work. The extension of the lifespan of rats is real and we fear that our error could delay or even prevent control experiments we are expecting to be made by others.

We have published on C60 toxicity since 1995 and all our results have been confirmed by several independent teams. . .

That point in the second paragraph is an important one: if these results are real, they're quite important and interesting. But, as with any other scientific result, they won't be accepted as real until they've been replicated, and replicating this experiment is already a substantial undertaking. The mistake with the figures doesn't help to get these started. (I should note that I've also called the authors' attention to the other points raised here in the comments).

My hope is that other groups studying longevity effects in rodents (and having already made the commitment that entails) will be able to add a C60 arm to their experiments as a comparison.

A couple of notes: in the previous post, I forgot to include the link to Wavefunction's article on the "negative rate constant" brouhaha - it's here, and well worth a look.

And I wanted to note that the post that discusses the Dobson and Kell theories about how compounds make their way into cells now has a comment from Douglas Kell himself, which is also worth a look if you're into this topic.

Over at The Curious Wavefunction, there's a great post looking back at the infamous "negative rate constant" affair (Breslow, Menger, Haim). If you're not familiar with that one, give it a look. I remember this one while it was going on, and in retrospect, you have to imagine what it would have been like if there had been a chemical blog world at the time. It's an extraordinary chapter in chemical (and chemical literature) history.

To that end, there's this opinion piece from yesterday's New York Times. Author Jack Hitt is talking about the tail of comments that now follows any notable article, in any field:

Almost any article worth reading these days generates some version of this long tail of commentary. Depending on whether they are moderated, these comments can range from blistering flameouts to smart factual corrections to full-on challenges to the very heart of an article’s argument. . .

Should this part of every contemporary article be curated and edited, almost like the piece itself? Should it have a name? Should it be formally linked to the original article or summarized at the top? By now, readers understand that the definitive “copy” of any article is no longer the one on paper but the online copy, precisely because it’s the version that’s been read and mauled and annotated by readers. (If a book isn’t read until it’s written in — as I was always told — then maybe an article is not published until it’s been commented upon.) Writers know this already. The print edition of any article is little more than a trophy version, the equivalent of a diploma or certificate of merit — suitable for framing, not much else.

I think this is exactly what science is about, and exactly what it needs. People should be able to read the latest results, add their opinions and criticisms to them, and those comments in turn should also be available for everyone to see. There's going to be noise in there, but I'll take some noise as the price that gets paid for figuring things out more quickly and more completely than we ever could before. As far as I'm concerned, the "peer" in "peer review" means "Everyone who can read and understand the paper".

Roche has halted trials of its CETP inhibitor dalcetrapib. Many will remember the Pfizer compound in this class, torcetrapib, which went down catastrophically in Phase III back in 2006. In that case, deaths in the treatment group were higher than the placebo group, which will bring you to a screeching halt every time. The generally accepted story is that the compound's effects on blood pressure (and possibly electrolyte balance) negated its beneficial effects on lipoproteins. But was torcetrapib actually working? It certainly raised HDL levels - but is that enough?

You have to wonder. Dalcetrapib wasn't taken out by toxicity - it was dropped because of "a lack of clinically meaningful efficacy". Analysis of several Phase II trials seems to have shown no beneficial outcome in cardiovascular mortality and mobidity. So what is it that we don't know about CETP, about HDL, and about lipoprotein roles in cardiovascular disease in general? Quite a bit, is my guess.

Two companies that are very, very much pondering that question are Merck and Eli Lilly, both with competing CETP inhibitors in the clinic. Expect statement from each of them that they continue to have confidence in their clinical candidates. But behind the scenes, expect a lot of very intense re-evaluation.

Now these are the funkiest structures I've seen in quite a while. I won't spoil the surprise; if you're an organic chemist, go ahead and click on the link. This is one of those "No one's made compounds like this, so let's see if they do anything" papers, and I'd say that if you're going to do that sort of thing, you should go pretty far off the beaten path. That they have.

These compounds are - not surprisingly - said to be cytotoxic, with activity against a range of cancer cell lines. A couple of passes through the paper, and I haven't found any normal cells used as controls for all that cytotoxicity. Sad to say, the betting would be that there's no window at all. But at least I've seen a class of compounds that I'll bet has never made it into J. Med. Chem. before.

Benlysta got approved for lupus last year, as the first new drug in the field in decades. But as noted at the time, it didn't exactly blow the doors out at the FDA, nor in the clinic. Now it's having a rough time in Europe, which makes things interesting for both Human Genome Sciences and their partners at GlaxoSmithKline.

Both the British (NICE) and German (IQWiG) agencies responsible for assessing the cost/benefit of new drugs have recommended against Benlysta's use. This adds some drama to GSK's recent offer of $2.6 billion for HGSI, which the smaller company turned down out of hand. Their case for a higher bid seems to be based on the market potential of Benlysta, but the arguing has begun over how realistic those hopes are. This is the sort of issue that gets settled with a sales price - or perhaps, in this case, just an upper bound. . .

Here's a Reuters headline for you: "GSK rejects idea of buying AstraZeneca".

In other news, Delta Airlines has rejected the idea of making its new fleet of long-range passenger jets out of bamboo and stale Fig Newton bars. There are also reports this morning that Burger King has rejected the idea of buying Birkenstock and cramming their sandals into buns in lieu of hamburger patties. More business news as it become available.

Here's an excellent piece by venture capital guy Bruce Booth, looking back at the heady days of 1991-1994. I can tell you that they weren't so heady in Big Pharma, but there were a lot of startups coming along. Included are some really big names of today, but also a lot of outfits that no one even remembers any more. And how have investors fared? That depends:

Only a subset of the 1991-1994 IPO window have accrued real value over time. There were certainly a few big winners in there – Gilead probably being the biggest, up over 100x since its IPO in 1992. MedImmune also fared quite well with its $16B acquisition (though AZ is not thrilled about it now), and Vertex is up 10x.

But let’s take the prior two examples, Isis and Amylin, which represent “successful” 20-year old mid-cap biotechs. Both have gone from preclinical stage companies around their IPOs to having products launched or filed with the FDA. But they haven’t really created any shareholder value over 20 years. Isis today trades at $8 per share, but it went public at $10 per share. Amylin went out at $14, but closed on the end of its first day of trading in 1992 at $21 per share. It now trades at $25. So for 20 years, these companies (and many, many others in the 1991-1994 cohort) have underperformed not only all major equity indices, but also treasury bills, and consumed billions in equity capital. And recall that many more companies from this window, probably at least half, ended up dying long whimpering deaths like long-forgotten Autoimmune Inc and Alpha-Beta Technology.

And that's a big reason why you don't see so many big biotech/small pharma IPOs any more. The markets are a different place, twenty years on:

The current reality, shaped by a couple decades of lackluster performance, is that the public markets aren’t open for business in biotech. While they are much less tolerant of the value-destroying tactics of the past (which is a good thing), they have also set the bar so high as to discourage even great, innovative companies from considering it as a viable option. In this new world, the old company building models just don’t work: it’s hard to back a startup today with an investment thesis around “we’re building the next Gilead” – the capital markets are just so different.

Small companies have to act differently, raise money differently, and sell themselves differently these days. Stay private, do as much virtually/outsourced, sell out to Big Pharma earlier than before. . .it's worth another post or two to talk about some of those models, but the "Let's Have an IPO!" one isn't going to be on the list. Not for some time to come, anyway.

Has the last shot been fired, very quietly, in the COX-2 discovery wars? Here's the background, in which some readers of this site have probably participated at various times. Once it was worked out that the nonsteroidal antiinflammatory drugs (aspirin, ibuprofen et al.) were inhibitors of the enzyme cyclooxygenase, it began to seem likely that there were other forms of the enzyme as well. But for a while, no one could put their hands on one. That changed in the early 1990s, when Harvey Herschman at UCLA reported the mouse COX2 gene. The human analog was discovered right on the heels of that one, with priority usually given to Dan Simmons of BYU, with Donald Young of the University of Rochester there at very nearly the same time.

The Rochester story is one that many readers will be familiar with. The university, famously, obtained a patent for compounds that exerted a therapeutic effect through inhibition of COX-2, without specifying what compounds those might be. They did not, in fact, have any, nor did they give any hints about what they'd look like, and this is what sank them in the end when the university lost its case against Searle (and its patent) for not fulfilling the "written description" requirement.

But there was legal action on the BYU end of things, too. Simmons and the university filed suit several years ago, saying that Simmons had entered into a contract with Monsanto in 1991 to discover COX2 inhibitors. The suit claimed that Monsanto had (wrongly) advised Simmons not to file for a patent on his discoveries, and had also reversed course, terminating the deal to concentrate on the company's internal efforts instead once it had obtained what it needed from the Simmons work.

That takes us to the tangled origin of the COX2 chemical matter. The progenitor compound is generally taken to be DuP-697, which was discovered and investigated before the COX-2 enzyme was even characterized. The compound had a strong antiinflammatory profile which was nonetheless different from the NSAIDS, which led to strong suspicions that it was indeed acting through the putative "other cyclooxygenase". And so it proved, once the enzyme was discovered, and a look at its structure versus the marketed drugs shows that it was a robust series of structures indeed.

One big difference between the BYU case and the Rochester case was the Simmons did indeed have a contract, and it was breach-of-contract that formed the basis for the suit. The legal maneuverings have been going on for several years now. But now Pfizer has issued a press release saying that they have reached "an amicable settlement on confidential terms". The only real detail given is that they're going to establish the Dan Simmons Chair at BYU in recognition of his work.

But there may be more to it than that. Pfizer has also reported taking a $450 million charge against earnings related to this whole matter, which certainly makes one think of Latin sayings, among them post hoc, ergo propter hoc and especially quid pro quo. We may not ever get the full details, since part of the deal would presumably include not releasing them. But it looks like a substantial sum has changed hands.

There's a new paper out in Cell Metabolism on resveratrol and SIRT1, and the press release from Elsevier (Cell Press) is just a tiny bit optimistic. "Study resolves controversy on life-extending red wine ingredient, restores hope for anti-aging pill", says the headline, but believe me, no one paper is going to do that. (This entry has links back to some of the history of the compound and the target, as covered here, but it's a convoluted story indeed). The EmbargoWatch web site calls it a "truly appalling" press release, and while I can't disagree with that, I don't think it particularly stands out: a lot of press releases are appalling.

And I disagree with them when they say that studies like this "probably don't deserve any coverage at all". It's actually a very interesting paper, even if it's not going to resolve any major controversies all by itself. It's from David Sinclair and co-workers (a large international team), and it presents the results of a long-running effort to see if what resveratrol does in animals that don't have the SIRT1 protein at all. That's a good experiment, which cuts right to the question of whether resveratrol's effects are SIRT1-driven or not. Problem is, the traditional knockout mouse model is almost always embryonic lethal in that case, so it's not so simple that generate such animals. The team was able to develop inducible whole-body conditional knockout adult mice, though, and set about dosing them with resveratrol to see what happened then.

Well, quite a few things did. From what I can see, the marquee items are these: normal mice fed a high-fat regimen showed beneficial effects on their mitochondria when given resveratrol, but the knockouts didn't, so that might be a clear connection to SIRT1. Resveratrol's effects on AMPK appear to be SIRT1-dependent (there are several links in this post about that connection, some of which led to papers that hypothesized a SIRT1-independent effect). But resveratrol treatment had good effects on glucose levels in mice, whether or not they had SIRT1 present, so that part seems to be going through some other pathway.

Sinclair's quoted in this Nature News piece as saying that this reflects the nature of resveratrol as a compound. “Resveratrol is a dirty, dirty molecule, very non-specific", he says. I think that's a very fair characterization, which is one of the reasons why I wouldn't take it myself. (That does shed an interesting light on the 2010 controversy when two former Sirtris executives set up their own reveratrol distribution effort, though, doesn't it?)

It would be quite interesting, for the sheer science of it, to take one of the later (apparently cleaner and more targeted) SIRT1 activating compounds that have come out of the GSK/Sirtris work and run it through the same animal model. You might expect the same sorts of SIRT1-driven effects, and perhaps much less of an effect on blood glucose, if that's really some off-target resveratrol thing. But since we're talking about epigenetic enzymes here, prediction is a chancy business. I wonder if this experiment is being done somewhere?

Just another nitpicking note: if you're going to publish a paper on glucose conjugates of drugs (aspirin, in this case), you might want to be sure to draw the glucose as the correct enantiomer. I had to do a little head-scratching with this one, since the sugar ring is drawn from a perspective that no carbohydrate chemist would ever use, but as far as I can tell, that's L-glucose instead of D. . .

This is not as big a deal in the grand scheme of things, but it particularly gets to me, as someone who worked with sugars as chiral starting materials for 4 1/2 years. And then, every chemical drawing program extant will draw you the correct stereochemistry. . .

Let's file this one under "Cultural Differences Between Chemists and Biologists". Have any of my chemistry colleagues out there noticed the difference in presentation detail between the two disciplines?

It's struck me several times over the years. Biologists seem, on average, to go into much more granular detail about their experiments when presenting to a mixed audience than do most chemists. Buffers, buffers that worked a little better, buffers that worked a bit worse, the brand of the sizing column, western blot after western blot. The usual chemistry comment was always "Hey, I don't show pictures of my TLC plates", but eventually I suppose we'll need to come up with another line as LC/MS takes over the world.

Even presenting among their own tribe, most chemists don't (to me) seem to go to the level of detail that I often see from protein purification people or pharmacologists. My theory is that most forms of biology still have so many hidden variables in them (since it's an intrinsically more complex and less understood science) that all the details need to be specified. Organic chemistry, for all its troubles, still tends to be more reproducible, on average, than molecular biology, and at a less picky level of detail

That's why chemists don't often feel the need to go into details even in a room full of chemists: "We had the bromide, so we made these coupled products, and then we made these by reductive amination. . ." substitutes for "We had the aryl bromide, so we reacted it with a list of boronic acids under palladium-catalyzed coupling conditions to give these products, each of which still has the aldehyde in the 3-position, which we purified by chromatography in an ethyl acetate/hexane gradient over 8-gram ISCO silica gel cartridges. We then reacted them with a list of amines using sodium triacetoxyborohydride in dichloromethane at room temperature, followed by a chromatography in 1 to 5% methanol/dichloromethane. . . ". Each of those steps has plenty of other options - different reagent combinations, solvents, etc., and if some colleague needs to reproduce your work, they'll check your notebook or ask you "Hey, what did you guys use for those Suzukis? Dppf? Yuck."

We certainly won't go into that level of detail in a room half full of biologists - it's mostly "We made these, and these, and these", which spares everyone. No TLC plates, no LC/MS traces, no NMR spectra. But they're available if you want 'em.

John LaMattina has a good piece up on the FDA, where they might be trying to have it both ways. About a recent speech by Janet Woodcock, he has this:

But Dr. Woodcock begins to stray into areas where I think she is off base. For one thing, she asserts that “many late stage [clinical] failures are due to efficacy problems.” That’s not exactly true. It is only when companies take compounds into late stage development with little or poor proof-of-concept data where this happens. The majority of phase 3 clinical trial failures are due to unforeseen, unpredicted side-effects or else due to finding that, in direct comparison to existing therapy, the new drug doesn’t show the superiority necessary to be successful commercially. Dr. Woodcock goes on to advocate for the generation of “evaluative tools,” new methodologies that can better predict the performance of a compound in late stage studies.

Of course, those tools are a good idea, and would be worth a lot (which is why everyone's been spending time and money trying to find them). But the FDA will not approve drugs based on them. They probably shouldn't - as LaMattina says, there have been quite a few drugs in recent years that looked like they would work based on one secondary endpoint or another, only to come up short in the real world. Woodcock is right to call for such approaches, but they won't necessarily shorten the time until approval. The hope is that they'll save time and money another way, in letting us kill projects earlier, with some hope of being right. Anything that spares us an unnecessary Phase II, or especially an unnecessary Phase III, is a good thing. But the eventual drug is going to have to jump through all the hoops, same as before.

There have been a number of headlines the last few days about Ranbaxy's Synriam, an antimalarial that's being touted as the first new drug developed inside the Indian pharma industry (and Ranbaxy as the first Indian company to do it).

But that's not quite true, as this post from The Allotrope makes clear. (Its author, Akshat Rathi, found one of my posts when he started digging into the story). Yes, Synriam is a mixture of a known antimalarial (piperaquine) and arterolane. And arterolane was definitely not discovered in India. It was part of a joint effort from the US, UK, Australia, and Switzerland, coordinated by the Swiss-based Medicines for Malaria Venture.

Ranbaxy did take on the late-stage development of this drug combination, after MMV backed out due to no-so-impressive performance in the clinic. As Rathi puts it:

Although Synriam does not qualify as ‘India’s first new drug’ (because none of its active ingredients were wholly developed in India), Ranbaxy deserves credit for being the first Indian pharmaceutical company to launch an NCE before it was launched anywhere else in the world.

And that's something that not many countries have done. I just wish that Ranbaxy were a little more honest about that in their press release.

So AstraZeneca's CEO is leaving. This wasn't necessary a voluntary move, but if it was, I don't blame him. I would have some serious thoughts about sticking around, too. (If reports of David Brennan's severance package have any truth in them, though, he'll have some time to figure out what to do next.)The company has major problems in its drug pipeline, has had major problems for a long time now, and no obvious fixes come to mind that won't take years of sustained effort.

Time for a reprise of this chart:

So how do drug molecules (and others) get into cells, anyway? There are two broad answers: they just sort of slide in through the membranes on their own (passive diffusion), or they're taken up by pores and proteins built for bringing things in (active transport). I've always been taught (and believed) that both processes can be operating in most situations. If the properties of your drug molecule stray too far out of the usual range, for example, your cell activity tends to drop, presumably because it's no longer diffusing past the cell membranes. There are other situations where you can prove that you're hitching a ride on active transport proteins, by administering a known inhibitor of one of these systems to cells and watching your compound suddenly become inactive, or by simply overloading and saturating the transporter.

There's another opinion, though, that's been advanced by Paul Dobson and Douglas Kell at Manchester, and co-workers. Their take is that carrier-mediated transport is the norm, and that passive diffusion is hardly important at all. This has been received with varying degrees of belief. Some people seem to find it a compelling idea, while others regard it as eccentric at best. The case was made a few years ago in Nature Reviews Drug Discovery, and again more recently in Drug Discovery Today:

All cells necessarily contain tens, if not hundreds, of carriers for nutrients and intermediary metabolites, and the human genome codes for more than 1000 carriers of various kinds. Here, we illustrate using a typical literature example the widespread but erroneous nature of the assumption that the ‘background’ or ‘passive’ permeability to drugs occurs in the absence of carriers. Comparison of the rate of drug transport in natural versus artificial membranes shows discrepancies in absolute magnitudes of 100-fold or more, with the carrier-containing cells showing the greater permeability. Expression profiling data show exactly which carriers are expressed in which tissues. The recognition that drugs necessarily require carriers for uptake into cells provides many opportunities for improving the effectiveness of the drug discovery process.

That's one of those death-or-glory statements: if it's right, a lot of us have been thinking about these things the wrong way, and missing out on some very important things about drug discovery as well. But is it? There's a rebuttal paper out in Drug Discovery Today that makes the case for the defense. It's by a long list of pharmacokinetics and pharmacology folks from industry and academia, and has the air of "Let's get this sorted out once and for all" about it:

Evidence supporting the action of passive diffusion and carrier-mediated (CM) transport in drug bioavailability and disposition is discussed to refute the recently proposed theory that drug transport is CM-only and that new transporters will be discovered that possess transport characteristics ascribed to passive diffusion. Misconceptions and faulty speculations are addressed to provide reliable guidance on choosing appropriate tools for drug design and optimization.

Fighting words! More of those occur in the body of the manuscript, phrases like "scientifically unsound", "potentially misleading", and "based on speculation rather than experimental evidence". Here's a rundown of the arguments, but if you don't read the paper, you'll miss the background noise of teeth being ground together.

Kell and Dobson et al. believe that cell membrane have more protein in them, and less lipid, than is commonly thought, which helps make their case for lots of protein transport/not a lot of lipid diffusion. But this paper says that their figures are incorrect and have been misinterpreted. Another K-D assertion is that artificial lipid membranes tend to have many transient aqueous pores in them, which make them look more permeable than they really are. This paper goes to some length to refute this, citing a good deal of prior art with examples of things which should have then crossed such membranes (but don't), and also find fault with the literature that K-D used to back up their own proposal.

This latest paper then goes on to show many examples of non-saturatable passive diffusion, as opposed to active transport, which can always be overloaded. Another big argument is over the agreement between different cell layer models of permeability. Two of the big ones are Caco-2 cells and MDCK cells, but (as all working medicinal chemists know) the permeability values between these two don't always agree, either with each other or with the situation in living systems. Kell and Dobson adduce this as showing the differences between the various transporters in these assays, but this rebuttal points out that there are a lot of experimental differences between literature Caco-2 and MDCK assays that can kick the numbers around. Their take is that the two assays actually agree pretty well, all things considered, and that if transporters were the end of the story that the numbers would be still farther apart.

The blood-brain barrier is a big point of contention between these two camps. This latest paper cites a large pile of literature showing that sheer physical properties (molecular weight, logP) account for most successful approaches to getting compounds into the brain, consistent with passive diffusion, while examples of using active transport are much more scarce. That leads into one of the biggest K-D points, which seems to be one of the ones that drives the existing pharmacokinetics community wildest: the assertion that thousands of transport proteins remain poorly characterized, and that these will come to be seen as the dominant players compared to passive mechanisms. The counterargument is that most of these, as far as we can tell to date, are selective for much smaller and more water-soluble substances than typical drug molecules (all the way from metal ions to things like glycerol and urea), and are unlikely to be important for most pharmaceuticals.

Relying on as-yet-uncharacterized transporters to save one's argument is a habit that really gets on the nerves of the Kell-Dobson critics as well - this paper calls it "pure speculation without scientific basis or evidence", which is about as nasty as we get in the technical literature. I invite interested readers to read both sides of the argument and make up their own minds. As for me, I fall about 80% toward the critics' side. I think that there are probably important transporters that are messing with our drug concentrations and that we haven't yet appreciated, but I just can't imagine that that's the whole story, nor that there's no such thing as passive diffusion. Thoughts?

Inspired by a discussion with a colleague, I'm going to take one more crack at the recent discussion here about the J. Med. Chem. DHFR paper. Those of you with an interest in the topic, read on. Those whose interest has waned, or who never had much interest to start with, take heart: other topics are coming.

It's clear that many people were disappointed with my take on this paper, and my handling of the whole issue. Let me state again that I mishandled the biology aspects of this one thoroughly, through carelessness, and I definitely owe this apology to the authors of the paper (and the readers of this site) for that.

Of course, that's not the only arguable thing about the way I handled this one. As I spent paragraphs rambling on about in yesterday's post, there's a chemical aspect to the whole issue as well, and that's what caught my eye to start with. I think one of the things that got me into trouble with this one is two different ways of looking at the world. I'll explain what I mean, and you can judge for yourself if I'm making any sense.

The authors of the paper (and its reviewer who commented here) are interested in D67 dihydrofolate reductase, from a biological/enzymological perspective. From this viewpoint - and it's a perfectly tenable one - the important thing is that D67 DHFR is an unusual and important enzyme, a problem in bacterial resistance, interesting in its own right as a protein with an odd binding site, and for all that, still has no known selective inhibitors. Anything that advances the understanding of the enzyme and points toward a useful inhibitor of it is therefore a good thing, and worth publishing in J. Med. Chem., too.

I come in from a different angle. As someone who's done fragment-based drug discovery and takes a professional interest in it, I'll take a look at any new paper using the technique. In this case, I gave the target much too cursory a look, and filed it as "DHFR, bacterial enzyme, soluble, X-ray structures known". In other words, a perfectly reasonable candidate for FBDD as we know it. Once I'd decided that this was a mainstream application of something I already have experience with, I turned my attention to how the fragment work was done. By doing so, I missed out on the significance of the DHFR enzyme, which means, to people in the first camp, that I whiffed on the most important part of the entire thing. I can understand their frustration as I brushed that off like a small detail and went on to what (to them) were secondary matters.

But here's where my view of the world comes in. As a drug discovery guy, when I read a paper in J. Med. Chem., I'd like to see progress in, well, the medicinal chemistry of the topic. That was the thrust of my blog post yesterday: that I found the med-chem parts of the paper uncompelling, and that the application of fragment-based techniques seemed to me to have gone completely off track. (I havne't mentioned the modeling and X-ray aspects of the paper, as Teddy Z did at Practical Fragments, but I also found those parts adding nothing to the worth of the manuscript as a whoel). The most potent compounds in the paper seem, to me, to be the sort that are very unlikely to lead to anything, and are unlikely to show selectivity in a cellular environment. If the paper's starting fragment hits are real (which is not something that's necessarily been proven, as I mentioned in yesterday's post), then it seems to me that everything interesting and useful about them is being thrown away as the paper goes on. From the other point of view, things are basically the opposite - the paper gets better and better as the compounds get more potent.

But here's where, perhaps, the two viewpoints I spoke of earlier might find something in common. If you believe that the important thing is that selective inhibitors of D67 DHFR have finally been discovered, then you should want these to be as potent and selective as possible, and as useful as possible in a variety of assays. This, I think, is what's in danger of being missed. I think that a fragment-based effort should have been able to deliver much more potent chemical matter than these compounds, with less problematic structures, which are more likely to be useful as tools.

I'll finish up by illustrating the different angles as starkly as I can. The authors of this paper have, in one view of the world, completed the first-ever fragment screen against an important enzyme, discovered the first-ever selective inhibitors of it, and have published these results in a prestigious journal: a success by any standard. From my end, if I were to lead a drug discovery team against the same enzyme, I might well see the same fragment hits the authors did, since I know that some of these are in the collections I use. But if I proceeded in the same fashion they did, prosecuting these hit compounds in the same way, I would, to be completely honest about it, face some very harsh questioning. And if I persevered in the same fashion, came up with the same final compounds, and presented them as the results of my team's work, I would run the serious risk of being fired. Different worlds.

Update: Prof. Pelletier sends the following:

If you feel any of this would be of interest for your blog, please feel free to post. Thanks for seeing this through rather than shaking it off.

So perhaps I should rethink all those nasty things I've been saying about Elsevier journals. Here's someone who submitted a paper to Nuclear Instruments and Methods on a Friday evening, and got it accepted - with two referee reports, yet - on Monday morning. How is that possible, you say? That's what this author is wondering, too. . .

The other day, I had some uncomplimentary things to say about a recent J. Med. Chem. paper on fragment-based dihydrofolate reductase inhibitors. Well, I know that I don't say these things into a vacuum, by any means, but in this case the lead author has written me about the work, and a reviewer of the paper has showed up in the comments. So perhaps this is a topic worth revisiting?

First, I'll give Prof. Joelle Pelletier of U. Montreal the floor to make the case for the defense. Links added are mine, for background; I take responsibility for those, and I hope they're helpful.

I was informed of your recent blog entitled ‘How do these things get published’. I am corresponding author of that paper. I would like to bring to your attention a crucial point that was incorrectly presented in your analysis: the target enzyme is not that which you think it is, i.e.: it is not a DHFR that is part of ‘a class of enzymes that's been worked on for decades’.

Indeed, it would make no sense to report weak and heavy inhibitors against ‘regular’ DHFRs (known as ‘type I DHFRs’), considering the number of efficient DHFR inhibitors we already know. But this target has no sequence or structural homology with type I DHFRs. It is a completely different protein that offers an alternate path to production of tetrahydrofolate (see top of second page of the article). It has apparently evolved recently, as a bacterial response to trimethoprim being introduced into the environment since the ‘60’s. Because that protein is evolutionarily unrelated to regular DHFRs, it doesn’t bind trimethoprim and is thus intrinsically trimethoprim resistant; it isn’t inhibited by other inhibitors of regular DHFRs either. There have been no efforts to date to inhibit this drug resistance enzyme, despite its increasing prevalence in clinical and veterinary settings, and in food and wastewater (see first page of article). As a result, we know nothing about how to prevent it from providing drug resistance. Our paper is thus the first foray into inhibiting this new target – one which presents both the beauty and the difficulty of complex symmetry.

Regular (type I) DHFRs are monomeric enzymes with an extended active-site cleft. They are chromosomally-encoded in all living cells where they are essential for cellular proliferation. Our target, type II R67 DHFR, is carried on a plasmid, allowing rapid dissemination between bacterial species. It is an unusual homotetrameric, doughnut-style enzyme with the particularity of having a single active site in the doughnut hole. That’s unusual because multimeric enzymes typically have the same number of active sites as they do monomers. The result is that the active site tunnel, shown in Figure 4 a, has 222 symmetry. Thus, the front and back entrances to the active site tunnel are identical. And that’s why designing long symmetrical molecules makes sense: they have the potential of threading through the tunnel, where the symmetry of the inhibitor would match the symmetry of the target. If they don’t string through but fold up into a ‘U”, it still makes sense: the top and bottom of the tunnel are also alike, again allowing a match-up of symmetry. Please note that this symmetry does create a bit of a crystallographer’s nightmare at the center of the tunnel where the axes of symmetry meet; again, it is an unusual system.

You have referred to our ‘small, poorly documented library of fragment compounds’. As for the poor documentation, the point is that we have very little prior information on the ligands of this new target, other than its substrates. We cast as wide a net as we could within a loosely defined chemical class, using the chemicals we have access to. Unfortunately, I don’t have access to a full fragment library, but am open to collaboration.

As a result of extending the fragments, the ligand efficiency does take a beating… so would it have been better not to mention it? No, that would have been dishonest. In addition, it is not a crucial point at this very early stage in discovery: this is a new target, and it IS important to obtain information on tighter binding, even if it comes at the cost of heavier molecules. In no way do we pretend that these molecules are ripe for application; we have presented the first set of crude inhibitors to ‘provide inspiration for the design of the next generation of inhibitors’ (last sentence of the paper).

Your blog is widely read and highly respected. In this case, it appears that your analysis was inaccurate due to a case of mistaken identity. I did appreciate your calm and rational tone, and hope that you will agree that there is redeeming value to the poor ligand efficiency, because of the inherent novelty of this discovery effort. I am appealing to you to reconsider the blog’s content in light of the above information, and respectfully request that you consider revising it.

Well, as for DHFRs, I'm guilty as charged. The bacterial ones really are way off the mammalian ones - it appears that dihydro/tetrahydrofolate metabolism is a problem that's been solved a number of different ways and (as is often the case) the bacteria show all kinds of diversity compared to the rest of the living world. And there really aren't any good D67 DHFR inhibitors out there, not selective ones, anyway, so a molecule of that type would definitely be a very worthwhile tool (as well as a potential antibiotic lead).

But that brings us to the fragments, the chemical matter in the paper. I'm going to stand my my characterization of the fragment library. 100 members is indeed small, and claiming lack of access to a "full fragment collection" doesn't quite cover it. Because of the amount of chemical space that can be covered at these molecular weights, a 200-member library can be significantly more useful than a 100-member one, and so on. (Almost anything is more useful than a 100-member library). There aren't more compounds of fragment size on the shelves at the University of Montreal?

More of a case could be made for libraries this small if they covered chemical space well. Unfortunately, looking over the list of compounds tested (which is indeed in the Supplementary Material), it's not, at first glance, a very good collection. Not at all. There are some serious problems, and in a collection this small, mistakes are magnified. I have to point out, to start with, that compounds #59 and #81 are duplicates, as are compounds #3 and #40, and compounds #7 and #14. (There may be others; I haven't made a complete check).

The collection is heavily biased towards carboxylic acids (which is a problem for several reasons, see below). Nearly half the compounds have a COOH group by my quick count, and it's not a good idea to have any binding motif so heavily represented. I realize that you intentionally biased your screening set, but then, an almost featureless hydrophobic compound like #46 has no business in there. Another problem is that some of the compounds are so small that they're unlikely to be tractable fragment hits - I note succinimide (#102) and propyleneurea (#28) as examples, but there are others. At the other end of the scale, compounds such as the Fmoc derivative #25 are too large (MW 373), and that's not the only offender in the group (nor the only Fmoc derivative). The body of the manuscript mentions the molecular weights of the collections as being from 150 to 250, but there are too many outliers. This isn't a large enough collection for this kind of noise to be in it.

There are a number of reactive compounds in the list, too, and while covalent inhibitors are a very interesting field, this was not mentioned as a focus of your efforts or as a component of the screening set. And even among these, compounds such as carbonyldiimidazole (#26), the isocyanate #82, and disuccinimidylcarbonate (#36) are really pushing it, as far as reactivity and hydrolytic stability. The imine #110 is also very small and likely to have hydrolytic stability problems. Finally, the fragment #101 is HEPES, which is rather odd, since HEPES is the buffer for the enzyme assays. Again, there isn't room for these kinds of mistakes. It's hard for me to imagine that anyone who's ever done fragment screening reviewed this manuscript.

The approach to following up these compounds also still appears inadequate to me. As Dan Erlanson pointed out in a comment to the Practical Fragments post, small carboxylic acids like the ones highlighted are not always legitimate hits. They can, as he says, form aggregates, depending on the assay conditions, and the most straightforward way of testing that is often the addition of a small amount of detergent, if the assay can stand it. The behavior of such compounds is also very pH-dependent, as I've had a chance to see myself on a fragment effort, so you need to make sure that you're as close to physiological conditions as you can get. I actually have seen some of your compounds show up as hits in fragment screening efforts, and they've been sometimes real, sometimes not.

But even if we stipulate that these compounds are actually hits, they need more work than they've been given. The best practice, in most cases when a fragment hit is discovered and confirmed, is to take as many closely related single-atom changes into the assay as possible. Scan a methyl group around the structure, scan a fluoro, make the N-for-C switches - at these molecular weights, these changes can make a big difference, and you may well find an even more ligand-efficient structure to work from.

Now, as for the SAR development that actually was done: I understand the point about the symmetry of the enzyme, and I can see why this led to the idea of making symmetrical dimer-type compounds. But, as you know, this isn't always a good idea. Doing so via flexible alkyl or alkyl ether chains is not a good idea, though, since such compounds will surely pay an entropic penalty in binding.

And here's one of the main things that struck both me and Teddy Z in his post: if the larger compounds were truly taking advantage of the symmetry, their ligand efficiency shouldn't go down. But in this case it does, and steeply. The size of the symmetical inhibitors (and their hydrophobic regions, such as the featureless linking chains, make it unsurprising that this effort found some micromolar activity. Lots of things will no doubt show micromolar activity in such chemical space. The paper notes that it's surprising that the fragment 4c showed no activity when its structural motif was used to build some of the more potent large compounds, but the most likely hypothesis is that this is because the binding modes have nothing to do with each other.

To be fair, compounds 8 and 9 are referred to as "poorly optimized", which is certainly true. But the paper goes on to say that they are starting points to develop potent and selective inhibitors, which they're not. The fragments are starting points, if they're really binding. The large compounds are dead ends. That's why Teddy Z and I have reacted as strongly as we have, because the path this paper takes is (to our eyes) an example of how not to do fragment-based drug discovery.

But still, I have to say that I'm very glad to hear a direct reply to my criticism of this paper. I hope that this exchange has been useful, and that it might be of use for others who read it.

Update: the paper has, for now, been pulled by JACS. More to come, no doubt.

I didn't written anything about the Breslow origins-of-chirality paper that mentioned, as a joking aside, the possibility of intelligent alien dinosaurs. As most readers will know, the ACS publicity office, most cluelessly, decided to make that throwaway line the focus of their press release, and much confusion ensued.

But things have gotten weirder. Stu Cantrill read the Breslow paper, and realized that he'd already read a lot of it before. See these three pictures (1, 2, 3) and realize the extent to which this latest paper was apparently a cut-and-paste job.

I've met Breslow many times (he used to consult for one of my former employers), and I've enjoyed reading much of his work. But this really shouldn't be acceptable - we wouldn't put up with it from some unknown chemist, and we shouldn't put up with it from someone famous. Chembark has an excellent summary of the situation, with recommendations about what the ACS should do next. These range from fixing that idiotic press release, to retracting the paper, to barring Breslow from publishing in JACS for a period.

In retrospect, the alien dinosaurs are becoming my favorite part of the whole paper.

Update: Breslow defends himself to Nature News.

I wanted to call attention to a piece by Bruce Booth over at Forbes. He starts off from the Scannell paper in Nature Reviews Drug Discovery that we were discussing here recently, but he goes on to another factor. And it's a big one: culture.

Fundamentally, I think the bulk of the last decade’s productivity decline is attributable to a culture problem. The Big Pharma culture has been homogenized, purified, sterilized, whipped, stirred, filtered, etc and lost its ability to ferment the good stuff required to innovate. This isn’t covered in most reviews of the productivity challenge facing our industry, because its nearly impossible to quantify, but it’s well known and a huge issue.

You really should read the whole thing, but I'll mention some of his main points. One of those is "The Tyranny of the Committee". You know, nothing good can ever be decided unless there are a lot of people in the room - right? And then that decision has to move to another room full of people who give it a different working-over, with lots more PowerPoint - right? And then that decision moves up to a group of higher-level people, who look at the slides again - or summaries of them - and make a collective decision. That's how it's supposed to work - uh, right?

Another is "Stagnation Through Risk Avoidance". Projects go on longer, and keep everyone busy, if the nasty issues aren't faced too quickly. And everyone has room to deflect blame when things go wrong, if plenty of work has been poured into the project, from several different areas, before the bad news hits. Most of the time, you know, some sort of bad news is waiting out there, so you want to have yourself (and your career) prepared beforehand - right? After all, several high-level committees signed off on this project. . .

And then there's "Organizational Entropy", which we've discussed around here, too. When the New, Latest, Really-Going-to-Work reorganization hits, as it does every three years or so, things slow down. They have to. And a nice big merger doesn't just slow things down, it brings everything to a juddering halt. The cumulative effect of these things can be deadly.

As Booth says, there are other factors as well. I'd add a couple to the list, myself: the tendency to think that If This Was Any Good, Someone Else Would Be Doing It (which is another way of being able to run for cover if things don't work out), and the general human sunk-cost fallacy of We've Come This Far; We Have to Get Something Out of This. But his main point stands, and has stood for many years. The research culture in many big drug companies stands in the way of getting things done. More posts on this to follow.

In Geneva, the (former) headquarters of Serono. They're transferring some of the jobs, but at least 500 are gone - and the people holding them are being put out into what (from here) looks like a very unfriendly jobs market. . .