As Arthur Kornberg never tired of pointing out, cells are gels. It’s too easy for biologists and chemists to imagine cells as sort of like liquid-filled plastic bags – and while that’s an OK picture as far as it goes, it tends to make you picture the cytoplasm as a lot more dilute than it really is. Something about the consistency of gumbo is more like it – maybe even the first batch of gumbo I ever made, to the whole pot of which I cluelessly added a good strong dose of filé powder, causing it all to set up into something could be nearly be sliced like a meat loaf.

The point is, there’s nowhere near as much bulk solvent in a cell as there is in anything you’d willingly work with in a lab. And that means that a lot of things behave differently than you expect – proteins, for example. Spherical proteins are the easiest to deal with, since they’re probably going to stay that way no matter what happens to them, short of outright denaturation. (Spheres are good choices for extreme environments). But most proteins aren’t spherical, and their shapes are extremely important – how well do we understand their behavior under real-world conditions?

It’s not an easy question to answer. The standard ways to study protein structures are (1) X-ray crystallography, a rather artificial state of affairs, since proteins are rarely found in the crystalline state in vivo, (2) NMR spectra, which can be very informative but are usually taken from purified proteins in a clean buffer solution, and (3) molecular modeling. That last technique’s relation to reality depends (among other things) on the patience, skill, and computational resources of the people using it. But just making sure that you’re modeling a protein’s structure in the presence of water molecules, rather than in some sort of ideal mathematical vacuum, can be enough of a challenge. Including a stew of other proteins right around the one of interest just isn’t feasible, even if we knew which ones to put in.

There’s a recent open-access paper in PNAS that does a good job calling attention to this problem. The authors studied a roughly football-shaped protein, VIsE, which comes from Borrelia burgdorferi, the Lyme disease organism. Diagnostic tests for Lyme recognize one stretch of this protein - but the odd thing is, that region appears to be buried inside the hydrophobic core of its structure, which makes you wonder how anything could recognize it at all.

The team studied the protein under different levels of denaturing agents and non-denaturing additives, and found several different structures seem to present themselves under different conditions. To their evident surprise, this even agreed with their molecular modeling of the process. Both the speed of protein folding and the courses the folding takes are altered - and under cellular levels of crowding, it turns out the protein may well adopt a spherical state that exposes much more of that antigen sequence. That's shown in the illustration, where C is the structure that's suggested for real-world conditions, as opposed to A, and the antigen sequence is shown in green. (The Y axis relates to the volume fraction taken up by various crowding agents).

Drug discovery people have always been wary of the structures of membrane-bound proteins, because we don't understand much about them. We should be wary of the structures of the free-swimming ones, too - after all, they're certainly wary of us.

As all organic chemists who follow the literature know, over the last few years there’s been a strong swell of papers using Barry Sharpless’s “click chemistry” triazole-forming reactions. These reaction let you form five-membered triazole rings from two not-very-reactive partners, an azide and an acetylene, and people have been putting them to all kinds of uses, from the trivial to the very interesting indeed.

In the former category are papers that boil down to “We made triazoles from some acetylenes and azides that no one else has gotten around to using yet, and here they are, for some reason”. There are fewer of those publications than there were a couple of years ago, but they’re still out there. For its part, the latter (interesting) category is really all over the place, from in vivo biological applications to nanotechnology and materials science.

One recent paper in Organic Letters which was called to my attention starts off looking as if it’s going to be another bit of flotsam from the first group, but by the end it’s a very different thing indeed. The authors (from the Isobe group at Tohoku University in Japan, with collaborators from Tokyo) have made an analog of thymine, the T in the genetic code, where the 2-deoxyribose part has both an azide and an acetylene built onto it.

So far, so good, and at one point you probably could have gotten a paper out of things right there – let ‘em rip to make a few poly-triazole things and send off the manuscript. But this is a more complete piece of work. For one thing, they’ve made sure that their acetylenes can have removable silyl groups on them. That lets you turn their click reactivity on and off, since the copper-catalyzed reaction needs a free alkyne out there. So starting from a resin-supported sugar, they did one triazole click reaction after another in a controlled fashion – it took some messing around with the conditions, but they worked it out pretty smoothly.

And since the acetylene was at the 5 position of the sugar, and the azide was at the 3, they built a sort of poly-T oligonucleotide – but one that’s linked together by triazoles where instead of the phosphate groups found in DNA. People have, of course, made all sorts of DNA analogs, with all sorts of replacements for the phosphates, but they vary in how well they mimic the real thing. Startlingly, when they took a 10-mer of their “TL-DNA” (triazole-linked) and exposed it to a complementary 10-residue strand of good ol' poly-A DNA, the two zipped right up. In fact, the resulting helix seems to be significantly stronger than native DNA, as measured by a large increase in melting point. (That's their molecular model of the complex below left).

Well, after reading this paper, my first thought was that it might eventually make me eat some of my other words. Because just last week I was saying things about the prospects for nucleic acid therapies (RNAi, antisense) - mean, horrible, nasty things, according to a few of the comments that piled up, about how these might be rather hard to implement. But when I saw the end of this paper, the first thing that popped into my head was "stable high-affinity antisense DNA backbone. Holy cow". I assume that this also crossed the minds of the authors, and of some of the paper's other readers. Given the potential of the field, I would also assume that eventually we'll see that idea put to a test. It's a long way from being something that works, but it sure looks like a good thing to take a look at, doesn't it?

You need access to vacuum if you’re going to work at the bench in chemistry. In fact, you need more than one kind. Reasonably hard vacuum (well, by our standards, which is laughable by the standards of the physicists) is down in the single Torr or below – that is, less than about 1% of normal air pressure. We use that for pulling out residues of water or organic solvents from our compounds. You can’t usually see it happening from the solid ones, but the syrupy liquids will foam up or blow a long series of thick bubbles when the vacuum is applied. The foam can be an irritating problem at times; some things will fill your flask with sticky bubbles and go right on up into the vacuum line if you’re not watching them.

The lesser vacuum lines are used for bulk evaporation of solvent (on your rotavap) and for filtering things off. We do an awful lot of both of those, too, and a full vacuum-pump pull is too vigorous for them in most cases. Evaporating down reactions is a constant task in an organic chemistry lab; I’d rather not think about how much of it I’ve done over the years. As for filtration, there are many cases where a solid product can be filtered out of the bulk liquid (which is good) or where some undesired solid by-product has to be filtered out before you can go on (not as good).

The low-tech way to get the sort of pull-it-though vacuum you need for these things is a water aspirator. You don’t see these as much any more, and you don’t see them at all in industry, since they necessarily pull solvent vapors into the water stream. But they work. An aspirator is basically a narrowing tube that hooks up to a hard-spraying water tap and has a sidearm fitting. The accelerating blast of water pulls the air in the tube along with it as it goes, creating a useful vacuum. If you wanted to make one rather more environmentally friendly, you’d keep a well-stocked dry ice condenser in line with it to trap out the solvent vapors before they go down the drain (which is what your rota-vap should have on it, anyway), but even with that, you’re always going to be turning the water flow into a waste stream. As I say, you don’t see them as much these days.

But we used them back when I was in grad school, that’s for sure, mostly for the rotavaps. If you wanted to keep things from splashing around back in your hood, you attached some rubber tubing to the other end of the thing and ran it further down the drain a bit.

Well, one day, one of the guys in the lab next door to me was shocked to see water blasting around in his hood. It was a real fountain, just geysering out full blast from what must have been a cracked water line or something in the back. He ran over and immediately shut off every tap – but to no avail. Roaring, showering water everywhere. Getting a look at the source, he realized, to his consternation, that the water was coming up out of the drain in the back of his hood. I remember standing there with him, staring at this in disbelief. It looked like a special effect. How on earth could you get water blasting up out of a drain pipe?

Suddenly it hit me. I ran around to the other side of the lab, where a new Japanese post-doc had taken up residence. “Masa”, I asked him, “Did you just put that rota-vap in your hood today?” “Yes, yes, just started it today”. There was a water aspirator flooshing away back in the back of his hood. “Did you put some rubber tubing on that thing?” “Tubing? Oh, yes” “How much?!” “Whoaaa. . .” He spread his arms to indicate the mighty extent of the rubber tubing he’d added.

Mighty, indeed. He’d run the stuff down his drain, through a horizontal pipe and right through a T joint, and back up out of the drain of the other guy’s hood, which backed on to his. So when he turned his water on full throttle, he immediately started irrigating his labmate’s space. We finally go thing turned off, and trimmed back the rubber tubing to a more reasonable length (like, not seven feet), and order was restored. For a while.

Note: if you want to see How Not To Do It to a really expensive vacuum rig, try here.

The Boston Globe has a piece on the open-source science movement. Many readers here will have come across the idea before, but it’s interesting to see it make a large newspaper. (Admittedly, the Globe is more likely to cover this sort of thing than most metropolitan dailies, given the concentration of research jobs around here).

The idea, as in open-source software development, is that everything is out in a common area for everyone to see and work on. (Here's one of the biggest examples). Ideas can come from all over, and with progress coming more quickly as many different approaches get proposed, debated, and tried out. I like the idea, in theory. Of course, since I work in industry, it’s a nonstarter. I have absolutely no idea of how you’d reconcile that model with profitable intellectual property rights, and I haven’t seen any scheme yet that makes me want to abandon profit-making IP as the driver of commercial science. Of course, there's always the prize model, which is worth taking seriously. . .

Even for academic science, open source work runs right into the traditional ideas of priority and credit, and the article doesn’t resolve this dilemma. (As far as I can tell, the open-source science advocates haven’t completely resolved it, either). There’s always the lingering (or not-so-lingering) worry about someone scooping your results, and for academia there’s always that little question of grant applications. There have been enough accusations over the years in various fields of people lifting ideas during grant proposal reviews or journal refereeing to make you wonder how well a broader open-source system would work out, given the small but significant number of unscrupulous people out there.

On the other hand, maybe if things were more open in general, there would be less incentive to lift ideas, since the opportunities to do so wouldn’t be so rare. And if someone’s name is associated from the beginning with a given idea, on some open forum, it could make questions of priority easier to resolve. A subsidiary problem, though, is that there are people who are better at generating ideas than executing them – some of these folks, once unchained, could end up with their fingerprints on all sorts of things that they’ve never gotten around to enabling. Of course, that might be a feature rather than a bug: people who generate lots of ideas are, after all, worth having around. And over time, there might well be less of a stigma than there is now for someone else to follow up on these things.

The thing is, science has already been a form of open-source work for hundreds of years now. It’s just that the information has been shared at a later stage, though presentations and publications, rather than being put out there right after it’s been thought up or while it’s being generated. That’s why I always shiver a bit when I read about how long Isaac Newton waited before writing up any of his results – if Edmund Halley hadn’t pressed him to do it, he might never have gotten around to it at all, which would have been a terrible tragedy.

And it’s why stories like those told of physicist Lars Onsager strike me as somehow wrong. Onsager was famous for only publishing his absolute best work – which was pretty damned good – and putting the rest into his copious file cabinets (example here). (A related trait was that he was also apparently incapable of lecturing at any comprehensible level about his work). Supposedly, younger colleagues would come by once in a while and tell him about some interesting thing that they’d worked out, and ask him if he thought it was correct. Onsager would pause, dig through his files, pull out some old unpublished work that the new person had unknowing duplicated, and say “Yes, that’s correct”. It seems to me that you don’t want to do that, withholding potentially useful results for the sake of what is, in the end, a form of vanity.

And although I'm not exactly Lars Onsager, this is as good a time as any to mention that my summer student, who’s finishing up in the lab this week, has been able to generate a lot of interesting data, and that I’m going to be trying to write it up this fall for publication. Readers may be interested to know that this work is based on more ideas I’ve had in the vein of the “Vial Thirty-Three” project detailed here, so with any luck, people will eventually be able to see some of what I’ve been so excited about all this time. And that’s about as open-source as this industrial scientist can get!

Many readers will well remember when Merck bought the RNA-interference company Sirna in 2006. They paid over a billion dollars for them, and made the whole RNA area an even bigger field for speculation than it was already.

Another big player in that field is Alnylam, who have been making deals all over the place. Many shareholders have been waiting for someone to buy ALNY for a similarly hefty premium, but the wait has been long (and all those agreements make such an acqusition harder and harder to realize).

As that post (and this one, and this one from 2004)) should make clear, I've been a bit cooler on the prospects for RNA therapies. I think the current RNA field is full of extremely interesting things, wonderful discoveries, fascinating research tools which could lead to all sorts of things - but I don't necessarily think it's full of new drugs per se. Nucleic acid-based therapies are just nightmarish to administer, and unless a real breakthrough in doing that appears, I think that (as drugs) they're always going to have their ankles tied together.

Well, Jonas Alsenas at Leerink Swann agrees, and he's not afraid to say so. According to Mike Huckman at CNBC, the firm initiated coverage of Alnylam with Alsenas saying that he thought the stock should be trading at about half its current value, and that he didn't see them developing any products for many years, if ever. And he went on to this statement, which I don't think anyone in the industry can deny:

The pharmaceutical industry is often swept by new technology fads. They are caused by sincere enthusiasm, fears of being left behind, and desperation to fill chronically depleted development pipelines, in our view.

I'm sure that the ALNY investors are not going to take this well, but hey, the truth hurts. For now, I continue to agree that modern RNA techniques are extraordinary research tools - but not drugs, not in almost every case.

Well, today’s subject isn’t a cheerful data set, but it certainly deserves some thought. Over at Pharmalot, Ed Silverman has some data from consulting firm AVOS Life Sciences, who have sat down to estimate how well various drug companies will do with revenue from new drugs over the next few years.

As of 2007, they have the industry average at about 77 cents coming from new products (defined as those launched within the previous five years) for every dollar lost from patent-expiring older ones. That doesn’t sound very good, but the average is a bit misleading, since it runs from the highs of Eli Lilly ($6.64/1), Amgen ($4.50/1) and Roche ($4.03/1) down to Sanofi-Aventis (11 cents new per dollar loss on the old). But it’s true that most everyone else is well under a dollar. It would be a lot of work, but it would be interesting to know (calculating by the same methods) how that ratio has changed over the last twenty years – that would give us some perspective on where we stand now.

But AVOS has gone out to estimate the picture in 2012, and it makes today’s numbers seem like a free buffet. Of the fourteen drug makers on their list, only Schering-Plough shows a robust increase in terms of how much it’s expected to make from new products versus its declining ones. GSK shows a modest improvement – and everyone else goes down.

That’s as in down, dooby doo, down down. The hardest-hit in terms of the actual numbers are Pfizer, AstraZeneca, Roche, and Sanofi-Aventis, all of whom are projected to be making pennies (or, gulp, nothing at all) from new products compared to what’s heading down the chute for them by then. In percentage terms, Roche and Eli Lilly are worst off – they look good now, as mentioned above, but the eventual losses of things like Zyprexa kick the ratios over good and hard. (Sanofi-Aventis goes down to zero, but only from that $0.11 figure, so it’s at least not going to be such an adjustment for them!)

As I say, I don’t have access to the underlying data, but the broad picture seems about right. There are a lot of big patent expirations coming up in the next few years, and not enough promising products coming on to replace them. According to AVOS, Roche and Sanofi-Aventis aren’t projected to have any new product launches at all between now and 2012, which can’t be good.

It’s worth remembering that figures like these are likely to show big swings even under normal conditions. Imagine a company with a big product that it launches, which gradually turns into a blockbuster. Near the end of its patent life, it launches another winner of the same type, which grows into another big seller. Everything’s fine! But the ratio of new revenue/expiring revenue is going to swing around a lot as you follow those sales numbers, sort of like derivatives in calculus, veering from too-high to too-low, although the company itself is sailing along pretty well. Let’s hope that this is some of the background for these numbers as well. The problem is, I don’t think that can explain all of them. . .

I wanted to recommend this post by Milkshake over at Org Prep Daily (and not just because he liked the recent column I wrote for Chemistry World). I was writing about the limited number of reactions that some med-chem labs get locked into, and the effect of this both on the compounds that get made, and on the motivation of the chemists. Milkshake has a good set of recommendations on how to avoid the boredom trap, and I recommend checking them out. He ends with the following:

You should care about the chemistry methodology and do things not just to crank out the final compounds to fill up the testing queue. Your boss (has) perhaps lost all his chemistry interest already and maybe he is unnerved about the project progress and pushes people hard - but while you try not to get fired you don’t necessarily want to think like your boss (and end up wretched). If you continue to look at your research project with curiosity and do things also for the sake of your chemistry interest you are likely to be more original because thinking about the methodology will suggest new directions in your medchem project. You may get accused of playing with chemistry and going off-tangent but you will likely remain more content and productive. . .

And this is all true. Most projects need some oddball compounds thrown into them, to keep things interesting (and honest), and it’s the people who are keeping up with the literature who will probably make them. I went through a period some years ago when I didn’t stay current with the journals very well, and if I’d let that continue to slide, it would have had a bad effect. (RSS was one of the things that saved me!)

But there’s another very good reason to stay sharp and run the unusual reactions, though: the boring reactions are increasingly going to be shipped to someone else, someone who probably works in a very different time zone. Yep, this is my “give ‘em something they can’t get in Shanghai” talk again. The outsourcing shops are there to pound out molecules as quickly as possible, and they’re going to use well-established chemistry as much as they can. Now, that’s the same pressure that operates in most med-chem projects, but I strongly recommend differentiating yourself if possible.

Be the person who runs the new stuff, who reads the literature and adopts things quickly, and who makes compounds that aren’t like all the stuff that’s already in the screening deck. You don’t have to go completely crazy, you know. There are plenty of good, reasonable structures that no one else is making at your company – have no doubt – and if you’re the person who makes them and who introduces new chemistry into the department, you have something with which to justify your salary (or a higher one!) On the other hand, if you’re the person who cranks out the sulfonamide libraries, well. . .they can get that cheaper somewhere else, you know.

So Genentech has told Roche to get lost – well, to a first approximation, anyway. I think what they’ve actually told them is to go open their Swiss wallets wider. What it comes down to now is how highly Genentech values itself versus how much Roche is willing to pay – the balance between those two will determine how things go. And then there are the large shareholders in Genentech to consider – if their idea of a good price clashes with the figure that Genentech’s board has in mind, then things could get more complicated. (And if the US dollar continues to climb against the Euro, that could complicated everyone's calculations, too - at the very least, it's speeding things up).

Personally, I think that Genentech is better off being left alone. But that’s no surprise – I think that in a lot of the M&A deals I’ve seen in the industry, particularly between large companies, I’ve thought that the participants should have stayed home and spent their money elsewhere. A personality defect, to be sure, and clear evidence that I’d never make it at an investment bank.

The reasons I think that Genentech is better off unmolested are probably the same ones that its own employees have. The company seems to have a good research culture going – they’ve been productive and willing to take risks, which is all you can ask of a drug discovery organization. Roche, for its part, isn’t exactly an Evil Empire, but they’re not Genentech. And that, I think, is what gets me about most of these deals. I think that there is no one best way to do drug discovery, since the problems we face are so varied. And that means that the more different approaches there are being tried, the better. We need a healthy ecology in this industry, and the closer we get to a monoculture, the worse off I think we’ll be. I think that Genentech has something to offer all its own, and that it’s in danger of being lost if Roche buys (and Roche-ifies) the place.

Some people out there are worried more than others. Roche doesn’t have as much experience in biologics, so they’ll want to retain the protein groups. (The question is whether they'll want to work for Roche!) But Genentech has also made a push into small molecules in recent years, and medicinal chemistry might be an area that Roche feels it has enough of already – they’re not buying Genentech for small molecules, after all. We’ll see over the next month if they’re buying Genentech at all. . .

Just wanted to let people know that yes, I'm still out here. I've returned from vacation, and am dealing with the usual catch-up on everything that's going on. That includes a flood of interesting data at work, thanks to my summer student, which is always nice to come back to!

Regular posting will resume on Monday, and we'll get back to what passes for normal around here.

I've just been told (by a reliable source) that something big is up with the Roche-Palo Alto site. I don't know if this is part of their bid for Genentech or what, but the word "closing" has been mentioned. I hate to pass on news like this with no more details, but something does appear to be going on. Anyone with more details, please add them in the comments section.

So much for not posting on my vacation - I haven't even finished packing for my flight yet. What a year this is for the industry, and it's only August. . .

I wanted to let people know that starting tomorrow I'll be taking some vacation time. Internet access will be rather limited - I'll be checking my mail some in the evenings, but there will be no posting until the middle of next week. Science will have to march on without me for a few days!

As mentioned in the comments here (and as told to me by e-mail as well), a lot of Genentech employees are looking around for other options in the face of a possible Roche takeover. A lot of Genentech employees – some other Bay area biotechs are apparently seeing shoals of CVs coming in. Does that ever give an acquiring company pause, when people start diving over the sides at its approach? I suppose it depends on if they’re in it to buy the current pipeline or to buy some research productivity. But surely Roche wants some of the latter? If they do finally succeed in buying Genentech, what will they have bought by the time they finish?

And while we’re on the job-seeking topic, I’ve heard about some possibilities for ex-GSK people (and others out on the market from the various recent layoffs). Merck is hiring at their West Point, PA site, for one. EMD-Serono is expanding and looking for people in Rockland, MA. And a rare drug-discovery opportunity outside the industry is also available at the NIH Chemical Genomics Center. I have contacts for these if people want to send in CVs directly - just e-mail me and let me know.

The ax is falling again at GlaxoSmithKline. This time it’s the oncology group.

Last month the cardiovascular people got this same treatment, you’ll recall, and there was some disagreement about how many jobs were being affected. But it looks like the company is moving one by one through its Centers of Excellence in Drug Discovery (CEDDs) and running a most excellent scythe through them. By the time they’re through, the total number of layoffs looks like it will be substantial indeed.

That’s because inside each area so far the cutbacks are pretty sweeping. Total oncology head count is apparently being reduced by about 40%. Discovery chemistry seems, unfortunately, to be getting it a bit worse, since some of the sub-areas aren't losing head count at all. The estimates I have are that of the c. 120 chemists in the area, about 60 are losing their jobs. That includes the entire oncology med-chem group at the Research Triangle Park location, and from what I'm told, none of them are being relocated to the Philadelphia-area sites. So much for discovering Tykerb, et al.

Are all of the CEDDs going to get this same treatment, or to the same degree? GSK isn’t saying, but I’d certainly bet on this sort of thing happening again as the year goes on. What the company’s research arm will look like when it’s all over is anybody’s guess, too, but there’s one thing for sure: it’ll be a heck of a lot smaller.

And whether this new trimmed-down inlicensed/outsourced GSK will be any more productive is anybody’s guess either. But we won’t know that for a long time. It’ll take quite a while just for all of these changes to stop reverberating through the company, for one thing, and then it’ll be several years after that before it’ll be possible to look at the pipeline and have a majority of it be a product of the new organization. As I’ve said before, this is one the biggest challenges in trying to engineer a large-scale change in a drug discovery shop – the lag time before you see the effects.

I’m already seeing resumes, but I’d like to invite any readers who know of openings for experienced drug discovery positions to either mention them in the comments or email me about them for a future post. (I did a lot of that during my own experience with a site closure, but of course, this time I don’t know most of the people involved personally). At the rate things are going, I’m going to have to start running classified ads down the right side of the page.

Today we take up the extremely interesting story of Rember, hailed in this week’s press as a potential wonder drug for Alzheimer’s. There are a lot of unusual features to this one.

To take the most obvious first, the Phase II data seem to have been impressive. It’s hard to show decent efficacy in an Alzheimer’s trial – you can ask Wyeth and Elan about that, although it’s a sore subject with them. But Rember, according to reports (this is the best I've seen), was significantly more effective than the current standard of care (Aricept/donezepil, a cholinesterase inhibitor). In light of some of the more breathless news stories, though, it’s worth keeping in mind that this was efficacy in slowing the rate of decline – not stopping it, and certainly not reversing it. Especially in the later stages of the disease, it’s extremely hard to imagine reversing the sort of damage that Alzheimer’s does to the brain (and yes, I know about the TNF-alpha reports – that subject is coming in a post next week). If Rember is twice as effective as Aricept, that's great - except Aricept's efficacy has never been all that impressive.

But that's still something, considering how the drug is supposed to work. Its target is different than the usual Alzheimer’s therapy. Accumulation of amyloid protein has long been suspected as the cause of the disease, but there have always been partisans for another pathology, the neurofibrillary tangles associated with tau protein. Arguments have been going on for years – decades – about which of these has more to do with the underlying cause(s) of Alzheimer’s. Rember is the first clinical shot (that I’m aware of) at targeting tau. If the first attempt manages to show such interesting results, it’s a strong argument that tau must be important. (Other people are working in this area, too, of course, but my impression is that it's nowhere near as many as work on amyloid).

That’s food for thought, considering the amount of time and effort that’s been expending on amyloid. It may be that both pathologies are worth targeting, or it may even be that these results with Rember are a fluke. But it’s also possible that tau is really the place to be, in which case the amyloid hypothesis will take its place in the medical histories as a gigantic dead end. I’m not quite ready to bet that way myself, but it’s definitely not something that can be ruled out. I wouldn’t put all my money on amyloid either, at this point. (Boy, am I glad I'm not still working in Alzheimer's: this sort of stuff is wonderful to watch from the outside, but from the inside it's hard to deal with).

Now, what about the drug itself? It’s coming from a small company called TauRx, whose unimpressive web site just went up recently. The underlying science (and the clinical data) all come from Dr. Claude Wischik of the University of Aberdeen, who has so far not published anything on the drug. The presentation this week has, by far, been the most that anyone’s seen of it (papers are said to be in the works).

And Rember itself is. . .well, it’s methylene blue. Now there’s an interesting development. Methylene blue has been around forever, used for urinary tract infections, malaria, and all sorts of things, up to treating protozoal infections in fish tanks. (For that matter, it’s turned up over the years as a surreptitious additive to blueberry pies and the like, turning the unsuspecting consumer’s urine greenish/blue, generally to their great alarm: a storied med school prank from the old days). What on earth is it doing for tau protein?

According to TauRx, the problem is that the aggregation of tau protein is autocatalytic: once it gets going, it's a cascade. They believe that methylene blue disrupts the aggregation, and even helps to dissociate existing aggregates. Once they're out in their monomeric forms, the helical tau fragments are degraded normally again, and the whole tau backup starts to clear out.

Now for another issue: there's been some commentary to the effect that Rember can't possibly make anyone any money, because it's a known compound. Au contraire. While we evil pharmaceutical folks would much rather have proprietary chemical matter, there are plenty of other inventive steps worth a patent. For one thing, I suspect that formulation will be a challenge here (and that Medpage story seems to bear this out). I doubt if methylene blue crosses the blood-brain barrier so wonderfully, and I also believe that it's cleared pretty well (thus that green urine). So TauRx had to dose three times a day, and their highest dose didn't seem to work, probably because of absorption issues. (That's also going to lead to gastrointestinal trouble). So formulating this ancient stuff so it'll actually work well could be a real challenge: t.i.d with diarrhea is not the ideal dosing profile for an Alzheimer's therapy, to put it mildly.

And for another, there's always mechanism of action. I deeply dislike patent claims that try to grab hold of an entire area, but there's so much prior art in tau that no one could try it. But use of a specific compound (or group of compounds) for a specific therapy: oh, yes indeed. It's a complicated area, and the law varies between Europe and the US, but it definitely can be done. The people who say that this can't be patented should check out the issued patents US7335505 or US6953794. Or patent applications US20070191352, WO2007110627, WO2007110629, and WO2007110630. There you go; that wasn't hard. Mind you, there might be some prior art for using such compounds as cognition-improving agents: I'd start here if I were in the business of looking into that sort of thing.

Finally, is methylene blue (or some derivative thereof) actually going to be a reasonable drug? There's that dosing problem, for one thing, but the long history in humans is encouraging (and is a key part of TauRx's hopes not to spend so much money on toxicity testing in the clinic - talks with the FDA should be starting soon). There have been contradictory reports (plus, minus) on the effects of the compound on the brain in general, though, so they may have to do more work than they're planning on. All in all, a fascinating story.

Note: I'm still working my way through the information on the much-hyped TauRx drug, Rember - a post on that is coming. Here's more from the same Alzheimer's meeting, though:

Elan and Wyeth unveiled the data on their widely anticipated Alzheimer’s drug bapineuzumab yesterday. This is another antibody from Elan’s shop, part of a long-running effort to induce an immune response to the amyloid protein which is thought to be a key player in the development of disease. And. . .well, this is an Alzheimer’s drug. That means it comes with all the standard baggage: it’s trying to treat an extremely difficult disease that we don’t understand very well, by a mechanism that no one can be sure will work or is even relevant. (Cue up this discussion from last week around here!)

This drug was always expected to have its best chance of working in patients without the APOE4 mutation, a lipoprotein which was identified in the 1990s as a significant risk factor for Alzheimer’s. Update: I shouldn't have used "always" there, since this was picked up during Phase II. But that shows that Wyeth and Elan did have it in mind as something to look for. The Phase III trials will, in fact, be stratified according to APOE4 status. And so it did – but not as dramatically as everyone had been hoping. About one-third of Alzheimer’s patients lack the APOE4 mutation, and this cohort showed slower decline in their brain functions with bapineuzumab treatment. But how much slower? The trial used a standard survey scale (ADAS-COG) – on that one, the existing Alzheimer’s drugs (Aricept, e.g.) show at most a 3-point effect, while bapineuzumab showed a five-point change.

That’s probably real, but I’m not sure how much that’s going to mean in the real world, and it’s certainly less than one would want. On top of that, the drug showed little or no benefit (and more side effects) in the two-thirds of the patients who have the APOE4 alleles, which meant that when all patients in the trial were taken together, improvement over placebo didn’t reach significance. And since this trial doesn’t seem to have been designed from the start to distinguish between those different patient groups, that’s the only number that you can take away with any certainty. All the other analyses are ex post facto, and thus carry less weight.

Investors, some of whom were clearly expecting a lot more than this, have not reacted well to the news: Elan’s drop has been taking the whole Irish stock exchange down along with it today. They have several other Alzheimer’s therapies in development, but the worries are starting to develop about the effectiveness of all the approaches that target amyloid. You can see some of those concerns being aired out in the latter half of the Forbes article. Some of the stronger statements are from people who are backing alternate hypotheses, which you should keep in mind, but there’s no doubt that the amyloid hypothesis for Alzheimer’s is still very much unproven. (Perhaps Lilly can shed some light today, but I doubt it, to tell you the truth). It’s going to be a long time before we can stop using that disclaimer that I had in the first paragraph.

I've talked about a lot of difficult therapeutic areas, but here's another boulevard of broken dreams: schizophrenia drugs. I was working on follow-ups to a promising clincial candidate, which has since been promising a number of times without ever delivering. It certainly missed its endpoints in schizophrenia by a mile in Phase II. That was actually my introduction to the drug industry back in 1989 - I followed that up with several years working on Alzheimer's, another notorious graveyard of good ideas, which makes me wonder why I didn't just quit at some point and open that chain of all-you-can-eat catfish restaurants that the Northeast so desperately needs.

Of course, once in a while a drug for dementia actually works a bit, and since there's a huge underserved market out there, it's a prize worth seeking (ask Lilly or J&J). But clinical success rates are absolutely horrific in the whole CNS area, and the latest company to demonstrate this is Vanda Pharmaceuticals in Maryland (I've always wondered if they're named after a spectacular, and spectacularly finicky, genus of orchid).

Vanda's drug iloperidone has been kicking around for years now. Hoechst Marion Roussel (now Aventis) seems to have discovered it in the early 1990s, and they, Novartis, and Titan have all handed it off to someone else over the years. Vanda was the last in line, but they got the dreaded "Not Approvable" letter from the FDA yesterday, and the company's stock was blitzed, down 73 per cent at the close. And the thing is, this drug got a lot closer than anything I used to work on. Vanda did hit their endpoints against placebo and against haloperidol, but the problem is, these are not necessarily the standard of care in schizophrenia:

" The FDA stated that Vanda had demonstrated the effectiveness of iloperidone at 24 mg/day in the 3101 study for which the company reported results in December, 2006, and that the efficacy was similar to the active comparator, ziprasidone (Geodon(R), Pfizer Inc.). In addition, the FDA also stated that iloperidone was superior to placebo in patients with schizophrenia at doses of 12-16 mg/day and 20-24 mg/day in a prior study. However, the FDA expressed concern about the efficacy of iloperidone in patients with schizophrenia relative to the active comparator, risperidone (Risperdal(R), Johnson & Johnson), used in prior studies. The FDA indicated that it would require an additional trial comparing iloperidone to placebo and including an active comparator such as olanzapine (Zyprexa(R), Eli Lilly & Company) or risperidone in patients with schizophrenia to demonstrate the compound's efficacy further. The FDA also stated that it would require Vanda to obtain additional safety data for patients at a dose range of 20 to 24 mg/day."

So iloperidone works, but quite possibly not well enough compared to what's already on the market. That alone won't quite sink your drug - you can always hunt for a patient cohort that benefits from a new compound, and you'll quite likely be able to find one if you have the resources. But as that last line mentions, there are additional safety concerns.

Reading between the lines, it would appear that iloperidone had the best chance of distinguishing itself in efficacy at the higher doses, but that the FDA wanted to make sure that side effects didn't start kicking in up there. This paper makes you wonder if one problem is the (dreaded) QT interval prolongation. Many other factors have looked relatively clean in some of the reported trials.

I greatly doubt if we'll see iloperidone surface again. Vanda wouldn't seem to have the resources, and too many other organizations have passed on it. At this point, it's hard to see why more money would be put into the compound. . .

1. “Hey, who dropped that condenser out on the floor in front of my hood? That looks just like the one I had on my reaction flask. . .”

2. “How come the toxicology people haven’t called me about our lead compound yet? Two-week tox finished a while ago, and usually they’re a lot faster than this. . . “

3. “Is there any active aluminum compound left in this reaction or what? I keep dripping methanol into it to quench it, and nothing’s going on at all so far. . .”

4. “Who’s going to scale up our candidate compound, anyway? We need 300 grams of the stuff, and the scale-up group is booked solid. . .”

5. “So, is this the high-pressure hydrogen line or the low-pressure one that I’m opening?”

6. “I wonder what the error bars are on that behavioral assay. . .”

Now for some belated Roche/Genentech comments: the first thing that I found surprising about this was that there was some surprise involved. Even though a move to buy the rest of Genentech has always been a possibility, the actual timing of the announcement seems to have been unexpected out in South San Francisco. But it probably had to be that way.

What alternative was there? Roche wouldn’t have made some announcement along the lines of “You know, we’re thinking about buying the rest of Genentech sometime pretty soon”, because that would have made the deal even more expensive as everyone piled into the stock. Regulation FD would mean that they really couldn’t give a heads-up to Genentech’s management without telling the world – after all, these are two separate companies, so it’s not an internal matter. So this had to be done just like any company making a bid for any other – with the difference being that Roche already had a head start on a majority of Genentech.

The second thing that occurred to me, though, was “why, and why now?” The first half of that question is answered, as are most “I wonder how come. . .” queries are, with the word “money”. Genentech has been coining the stuff, and Roche would like to have all that revenue instead of just part of it. “Why now” comes down to money, too. The two companies were due to renegotiate their revenue sharing in 2015, and Roche apparently decided (among other factors) that the US dollar was about as cheap as it was going to get. You could turn the question around and ask why Roche took the whole don't-own-it-all approach in the first place. (They did own it all for a while, but put Genentech back out into the market in 1999).

I always assumed that they were worried about messing up whatever it was that had Genentech doing so well in the first place. If true, that showed an admirable level of self-knowledge on Roche’s part. Too many other companies seem to assume that the outfits that they buy will be just fine under the new letterhead – even better, probably, now that they’ve been bought by such a fine bunch of people! But it certainly doesn’t always work out that way. The challenge is to keep the acquired company, and its culture, from dissolving into the larger one like a sugar cube. (The alternative is to just buy companies for their physical or IP assets, not giving a hoot for who might be working there, and we’ve seen plenty of that, too).

But Genentech is a mighty big sugar cube, and it’s a long way from the rest of Roche’s operations. I’d guess that the folks in Basel are planning (hoping) that Genentech will go on just like it has, just with a few accounting adjustments (like all the money ending up on Roche’s books). There are probably a lot of reassuring messages going out to the Genentech people about how gosh, we already had a majority interest in you, so this is just sort of a formality, and it’ll probably save lots of money besides, you know, so just keep right on doing what you’re doing. . .

We’ll see. The Swiss are not known for their delicate managerial touch. One solution that's been talked about would be (once Roche has Avastin et al. safely booked) for them to spin out a new version of Genentech as a publicly traded company again - 1999 all over again. And we'll see if Genentech even goes for the offer - there's a lot of doubt about that, at least at the price the Roche is offering. They've apparently opted out of the provisions in the 1999 agreement about how Roche could buy them, so all sorts of things are now possible. . .

I’m going to expand on one of the points brought up yesterday, about the reported drug industry executive who was confident that his company’s Alzheimer’s therapy was ready to go out and make billions of dollars. It was that word “confident” that set me off, I think.

Because that’s not a word that you hear much of in this industry. The strongest form that you’ll come across is something like “fairly confident”, which is how you feel when you send in a compound that’s a minor change off something that’s already active, or how you feel about screening a target that’s a close homologue of something you already have plenty of ligands for. You can be pretty sure in those cases that something’s going to hit – but you’ll note that both of those are pretty far upstream in the drug discovery process. As you move toward animals, that confidence begins to look pretty ragged, and depending on the disease, it can just flat-out evaporate.

Despite all our efforts to avoid the expensive little beasts, there is still no way to be sure about how your compound is going to act in an animal until you’ve put it into an animal. That goes for predicting its peak blood levels, its half-life, its metabolites, and the duration and degree of its efficacy. You can have your compounds all ranked in order of how you think they’ll perform, and that list will, every time, be reordered after a first round of animal testing.

And when you go further, you really have no idea. As I’ve said here before, if you don’t cross your fingers when you take a compound into two-week toxicity testing, you haven’t been doing this stuff very long. Despite all efforts to avoid this expensive step, two-week (and four-week and longer) tox testing in animals will always, always tell you things you didn’t know. (Most of the time it’ll tell you things you didn’t particularly want to hear). No one worth their salary will ever use the adjective “confident” before the first multiweek tox data come in.

So much for animals: how about people? Well, despite all our efforts, there are still surprises in Phase I dosing, the tip-toe clinical stage where you look for blood levels in healthy volunteers. The animal pharmacokinetic data tell you where to start the doses in humans, but you can still get ambushed. I worked on a receptor agonist project once where the human blood levels came back at just about 10% of what we’d predicted, so back to the drawing board we went. No, I’ve never heard anyone describe themselves as “confident” before Phase I.

And that’s an easy step compared to Phase II, where for the first time you put your drug into sick patients. The failure rate in Phase II is just abominable, and stands as an indictment of just how little we understand about the biochemistry of human disease and how to modify it. When you consider a central nervous system disease like Alzheimer's, the source of the "confident" quote that started this digression, the failure rate is over 90%. Our understanding of the causes and progression of Alzheimer's is very poor. That's as opposed to a more well-worked-out condition like, say, hypertension, where our understanding is merely quite inadequate.

But if you make it through that fine sieve, you move on to Phase III, a larger and more real-world look at the patient population. If your Phase II trial was designed to provide a robust test, rather than just to make you and your investors feel good, you can hope that your Phase III will work out. But the whole time it's going on, the prudent drug developer will remember that the biggest, most well-funded, and most competent research organizations in the world have all taken huge cratering dives in Phase III. You know a lot more about your compound by this stage, so these disasters don't happen as often - but that means that when they do, they rise right up out of the floor in front of you. No, you can feel better by Phase III, but "confident" is pushing it.

How about when your drug goes to the FDA? Try asking any drug company executive if they'd like to go on record as being "confident" of regulatory approval. And when your drug actually goes to market? Is anyone really confident about those projections from the people in marketing? Pfizer sure talked a good game about Exubera, remember. Don't forget, too, that nasty side effects can always be waiting out there in the larger patient population. Even after your drug goes out and starts earning a living, it can be completely torpedoed at any time. Baycol, Vioxx, Avandia - you can name more.

So that's the story: you can never kick back and relax in this business. For all the perception that some people have of the drug industry as a sure-fire money machine, it sure doesn't look that way from inside. Anyone who describes themselves as "confident" about their new experimental medication is trying to fool their listeners. Or themselves. Maybe both.

A longtime reader sent along a very interesting example that’s being used in a new book. The Gridlock Economy by Columbia economist Michael Heller is getting some good press, including this interview over at the Wall Street Journal>’s Law Blog. Heller’s thesis is:

“When too many owners control a single resource, cooperation breaks down, wealth disappears and everybody loses.” That is, the gridlock created by too much private ownership is wreaking havoc on our economy and lives. It’s keeping badly needed runways from being built, stifling high-tech innovation, and “costing lives” by keeping groundbreaking drugs from hitting the market.

It’s that last example that caught the eye of my correspondent, and I wanted more details. Fortunately, Heller went on the in the interview to talk about that very case, and I’m going to just quote him on it:

”Here’s a life or death example that’s happening right now: A drug company executive tells me he may have a better Alzheimer’s treatment. But to get FDA approval and bring it to market, he has to license dozens and dozens of patents relevant to testing for safety and side effects. So negotiations fail and the Alzheimer’s drug sits on a shelf, even though my informant is confident it could save countless lives and earn billions of dollars.”

Now, here’s the problem: I’ve actually worked on Alzheimer’s disease myself, and this story does not ring true. I don’t know if Heller’s “informant” is talking about animal testing or clinical trials in humans, but the same points hold in both cases. For one thing, I’m not aware of any patents that have to be licensed to do the standard testing for safety and side effects. There could conceivably be a couple for faster or more convenient tests, but I don’t even know of those. Otherwise, safety testing, in both animals and humans, is (to the best of my knowledge) done pretty much outside the realm of patent considerations. That “dozens and dozens of patents” line seems wildly off to me. I have never heard of a drug (for any disease) that has not advanced due to patent considerations related to safety testing.

Update - and that's partly for a very good legal reason: the safe harbor provisions of the 1984 Hatch-Waxman Act, as reaffirmed in the 2005 Merck v. Integra decision by the Supreme Court. There is specific protection from infringement in the use of a patented compound for purposes of submitting regulatory filings. And the language of the ruling makes it look like it's intended to cover all sorts of patented technologies as well.

Second, it’s important to remember that efficacy testing comes after safety, at least when you get to humans. So this contact of Heller’s is talking about a drug that has not been evaluated in humans for either quality, but he’s still “confident it could save countless lives and earn billions of dollars”. Right – for Alzheimer’s, where you have to worry about human brain levels, where we’re still arguing about what even causes the whole disease, where the clinical trials take years because the deterioration is so slow. Professor Heller is being had.

And let’s stipulate that there are, somehow, enough convincing data to make a reasonable observer confident that said drug would go on to earn billions of dollars. (There is never enough information to completely convince anyone of that in this industry before a drug hits the market, but let’s pretend that there is). In that case, those mysterious patent negotiations would not fail. Some sort of agreement would be reached, with money like that on the table.

The problem with Heller using this example is that there are indeed a lot of problems and potential problems with intellectual property in the drug industry. (I’ve talked about a few of them here). It’s a big, important, complicated, topic – and for all I know, it gets a good treatment in Heller’s book. (I’ll read it and find out). But this cartoon of an example is going to confuse anyone outside the field, and irritate anyone inside it.

Merck took the unusual step of delaying its earnings release yesterday until after the close of the market. A report on another clinical study of Vytorin (ezetimibe), their drug with Schering-Plough, was coming out, so they put the numbers on hold until after the press release yesterday afternoon. Naturally, this led to a lot of speculation about what was going on. A conspiracy-minded website vastly unfriendly to Schering-Plough suspected some sort of elaborate ruse to drum up publicity.

But that sort of thinking doesn't take you very far, unless you count the distance you rack up going around in circles. As it turned out, the SEAS trial (Simvastatin and Ezetimibe in Aortic Stenosis) was, in fact, very bad publicity indeed for the drug and for both companies. In fact, a real conspiracy would have made sure that these numbers never saw the light of day, or were at least released at 6 PM on a Friday. But no, the spotlight was on them good and proper.

This trial studied patients with chronic aortic stenosis, which is a different condition than classic atherosclerosis. The two have enough similarities, though, that there has been much interest in whether statin treatment could be effective. The primary endpoint, a composite of aortic valve and general cardiovascular events, was missed. Vytorin was no better than placebo. It reached significance against one secondary endpoint, reducing the risk of various ischemic events, but not in any dramatic fashion.

That's not necessarily a surprise, since there's not a well-established therapy for aortic stenosis (thus the trial design versus placebo). As several commenters to the conference call after the press conference pointed out, this shouldn't change clinical practice much at all. But it's not what Merck and Schering-Plough needed to hear, that's for sure, because the sound bite will be "Vytorin Fails Again".

Actually, the sound bite will be even worse than that. There are a lot of headlines this morning about another observation from the SEAS trial: that significantly more patients in the treatment arm of the study were diagnosed with cancer. That's a red warning light, for sure, but in this case we have at least some data to decide how much of one.

For one thing, as far as I know there have been no reports of increased cancer among the patients taking Vytorin out in the marketplace - of course, one could argue that this might have been missed, but if the effect were as large as seen in the SEAS study, I don't think it would have been. Analyses of the earlier Vytorin trials and the ongoing IMPROVE-IT trial versus Zocor have also shown no cancer risk, and the latter trial is continuing. So for now, it would appear that either this was a nasty result by chance, or (a longer shot) that there's something different about the aortic stenosis patients that leads to major trouble with Vytorin.

None of these scientific and statistical arguments, and I mean none of them, will avail Schering-Plough and Merck. Among people who've heard of Vytorin at all, the first thing that will come to mind is "doesn't work", and after today's headlines, the second thing that will come to mind is "cancer". Just what you want, to put out press releases that your compound, even though it failed to work again, isn't actually a cancer risk. You really couldn't do worse; a gang of saboteurs couldn't have done worse. Of course, there's no such gang: the companies themselves authorized these trials, thinking that there were home runs to be hit. But all these sidelines - familial hypercholesteremia, aortic stenosis - have only sown fear, confusion, and doubt. The only thing that I can see rescuing Vytorin as a useful drug is for the IMPROVE-IT results to show really robust efficacy in its real-world patients. And I wonder if even that could be enough.

One of the things that no one realizes about research (until they’ve done some) is how much time can be spent going back over things. Right now I’m fighting some experiments that should be working, have worked in the past, but have (for some reason) decided not to work at the moment. Irritating stuff. There’s a reason buried in there somewhere, and when I find it things will be that much more robust in the future, but I’d hoped that they were that solid already.

And across the hall, a check is going on of some screening hits. When you get a pile of fresh high-throughput screening data, including some fine-looking starting compounds for a new project, what do you do with it? Well, if you have some experience, the first thing you do is order up fresh samples of all the things you could possibly be interested in, and check every single one of them to make sure that they actually are what they say on the label. Don’t start any major efforts until this is finished.

In fact, you should order up solid samples from the archives along with some of the DMSO stock solution that they used in the screening assay. They might not be the same, not any more. False negatives and false positives are waiting in your data set, depend on it: compounds that should have hit, but didn’t because they decomposed in solution, and compounds that (sad to say) did hit only because they decomposed in solution. You’ll probably never know about the first group, and you can waste large amounts of time on the second unless you check them now.

Getting a project going, then, can seem like trying to get a dozen nine-year-olds into a van for a long trip. Someone’s always popping out again, having forgotten something, which reminds someone else, and your scheduled departure time arrives with everyone running in circles around the driveway.

But nine-year olds can eventually be corralled, as can the variables in most scientific projects. But not always. Where you don’t want to be is the situation people had with the early vacuum-tube computers. Vacuum tubes have not-insignificant failure rates. So if you have, say, twenty thousand of the little gizmos in your ENIAC or whatever, doing the math on mean-time-between-failures shows you that the thing can run for maybe forty-five minutes before blowing a tube (unless you take heroic measures). And the more vacuum tubes you have, the worse the problem gets: make your computer big enough, and it’ll blow right after you throw the switch, every time.

So that’s the other thing you have to watch when troubleshooting: try to make sure that your problems aren’t built into the very structure of what you’re trying to do. In med-chem projects, look out for statements like “we have all the activity we need, now we just need to get past the blood-brain barrier”. Sometimes there’s a way out of those tight spots, but too often the properties that (for example) could get your compound into the brain are just flat incompatible with the ones that gave you that activity in your assay. You’d have been better off approaching that combination the other way around, and better off realizing that months ago. . .

Here’s an appropriate topic for a Friday, although at first many of you may think I’ve lost my mind. What would happen if you combed the full text of the experimental sections of the chemistry journals, looking for how long people ran their reactions?

I’m pretty sure that I know what you’d see: there would be a lot of scatter in the short time periods, with some peaks at the various half-hour and hour marks just for convenience. But as you went out into the multiple-hour procedures, I feel sure that you’d see pronounced spikes in the data at around sixteen to twenty hours and again at around 72 hours.

Some readers have doubtless started nodding their heads, having done the math. Those times correspond to "overnight" and "over the weekend", and I'm willing to bet that they're over-represented (and how) in the data set. I'll go on to predict scarce examples in, say, the 14-hour or 38-hour ranges - there's not much way to run a reaction for those intervals and not be in the lab too early in the morning or too late at night.

A second-order prediction is that when such reactions are found, that their origins will skew heavily toward academia rather than industry. And I'm also willing to bet that patent procedures will tend to follow the working-day timelines more than the general literature, for the same reasons. My last higher-order prediction is that the reaction times would not, in fact, obey Benford's Law, as many other data sets of this kind do.

As far as I know, no one's ever done this sort of analysis, but I suppose it would be possible, especially for someone at Chemical Abstracts or at one of the scientific publishers. If someone wants to try it, please let me know what comes out. And if the results follow my predictions, please feel free to refer to the title of this post or something similar. I won't object.

At various points in my drug discovery career, I’ve worked on G-protein-coupled receptor (GPCR) targets. Most everyone in the drug industry has at some point – a significant fraction of the known drugs work through them, even though we have a heck of a time knowing what their structures are like.

For those outside the field, GPCRs are a ubiquitous mode of signaling between the interior of a cell and what’s going on outside it, which accounts for the hundreds of different types of the things. They’re all large proteins that sit in the cell membrane, looped around so that some of their surfaces are on the outside and some poke through to the inside. The outside folds have a defined binding site for some particular ligand - a small molecule or protein – and the inside surfaces interact with a variety of other signaling proteins, first among them being the G-proteins of the name. When a receptor’s ligand binds from the outside, that sets off some sort of big shape change. The protein’s coils slide and shift around in response, which changes its exposed surfaces and binding patterns on the inside face. Suddenly different proteins are bound and released there, which sets off the various chemical signaling cascades inside the cell.

Naturally, there are at least two modes of signaling a GPCR can engage in: on and off. A ligand that comes in and sets off the intracellular signaling is called an agonist, and one that binds but doesn’t set off those signals is called an antagonist. Antagonist molecules will also gum up the works and block agonists from doing their things. We have an easier time making those, naturally, since there are dozens of ways to mess up a process compared to the ways there are of running it correctly!

Now, when I was first working in the GPCR field almost twenty years ago, it was reasonably straightforward. You had your agonists and you had your antagonists – well, OK, there were those irritating partial agonists, true. Those things set off the desired cellular signal, but never at the levels that a full agonist would, for some reason. And there were a lot of odd behaviors that no one quite knew how to explain, but we tried to not let those bother us.

These days, it’s become clear that GPCRs are not so simple. There appear to be some, for example, whose default setting is “on”, with no agonist needed. People are still arguing about how many receptors do this in the wild, but there seems little doubt that it does go on. These constituitively active receptors can be turned off, though, by the binding of some ligands, which are known as inverse agonists, and there are others, good old antagonists, that can block the action of the inverse agonists. Figuring out which receptors do this sort of thing - and which drugs - is a full time job for a lot of people.

It’s also been appreciated in recent years that GPCRs don’t just float around by themselves on the cell surface. Many of them interact with other nearby receptors, binding side-by-side with them, and their activities can vary depending on the environment they’re in. The search is on for compounds that will recognize receptor dimers over the good ol’ monomeric forms, and the search is also on for figuring out what those will do once we have them. To add to the fun, these various dimers can be with other receptors of their own kind (homodimers) or with totally different ones, some from different families entirely (heterodimers). This area of research is definitely heating up.

And recently, I came across a paper which looked at how a standard GPCR can respond differently to an agonist depending on where it's located in the membrane. We're starting to understand how heterogeneous the lipids in that membrane are, and that receptors can move from one domain to another depending on what's binding to them (either on their outside or inside faces). The techniques to study this kind of thing are not trivial, to put it mildly, and we're only just getting started on figuring out what's going on out there in the real world in real time. Doubtless many bizarre surprises await.

So, once again, the "nothing is simple" rule prevails. This kind of thing is why I can't completely succumb to the gloom that sometimes spreads over the industry. There's just so much that we don't know, and so much to work on, and so many people that need what we're trying to discover, that I can't believe that the whole enterprise is in as much trouble as (sometimes) it seems. . .

Now, if I were still doing metabolic disease work, I'd be all over this target: CAMKK2, which is mercifully short for "Ca2+/calmodulin-dependent protein kinase kinase 2". (Kinase nomenclature has been out of hand for years, in case you're wondering).

CAMKK2 is right in the middle of a lot of pathways that are known to be important for regulation of appetite and glucose levels, namely ghrelin, AMPK, and NPY. These have been rather hard to approach directly with small molecules, or (in the case of NPY) hitting them hasn't been enough by itself. That's the problem with a lot of potential therapies for obesity, as I've mentioned here before. As a behavior, eating is full of overlapping backup redundant pathways, since we're all descendants of creatures that ate whatever they could, whenever they could. The ones whose feeding could be easily shut down or interrupted didn't make it this far.

So even though the field is littered with things that haven't worked out, perhaps a target like this, which seems to be more upstream, might have a better chance of success. We're definitely going to find out. Given the number of companies interested in this area, and the number with kinase expertise, someone's going to be able to take a good swing at this one. The benefits might go beyond weight loss - animals given a known inhibitor (STO-609, a Sumitomo compound) were also resistant to the bad effects of a high-fat diet, putting on less weight than controls and showing better glucose control.

Of course, the fact that Sumitomo had a compound years ago that hits this target so well makes you wonder what ever happened to it. I can't find much about why it didn't progress, but you can be sure that other people are asking that same question right now. . .Update: see this comment for more on this topic. . .

Cyanogen bromide is not a nice reagent. It’s not quite on my list of things that I refuse to use, but it’s definitely well up on the list of the ones I’d rather find an alternative to. The stuff is very toxic and very volatile, and reactive as can be.

But it’s not the worst thing in its family. A good candidate for that would be cyanogen azide, which you get by reacting the bromide with good old sodium azide. Good old sodium azide, which is no mean poison itself, will do that with just about any bromide that’s capable of being displaced at all. Azide is one of the Nucleophiles of the Gods, like thiolate anions – if your leaving group doesn’t leave when those things barge in, you need to adjust your thoughts about it. Cyanogen bromide (or chloride) doesn't stand a chance.

Cyanogen azide is trouble right from its empirical formula: CN4, not one hydrogen atom to its name. A molecular weight of 68 means that you’re dealing with a small, lively compound, but when the stuff is 82 per cent nitrogen, you can be sure that it’s yearning to be smaller and livelier still. That’s a common theme in explosives, this longing to return to the gaseous state, and nitrogen-nitrogen bonds are especially known for that spiritual tendency.

There were scattered reports of the compound in the older German and French literature, but since these referred to the isolation of crystalline compounds which did not necessarily blow the lab windows out, they were clearly mistaken. F. D. Marsh at DuPont made the real thing in the 1960s (first report here, follow-up after eight no-doubt-exciting years here). It's a clear oil, not that many people have seen it that state, or at least not for long. Marsh's papers are, most appropriately, well marbled with warnings about how to handle the stuff. It's described as "a colorless oil which detonates with great violence when subjected to mild mechanical, thermal, or electrical shock", and apologies are made for the fact that most of its properties have been determined in dilute solution. For example, its boiling point, the 1972 paper notes dryly, has not been determined. (The person who determined it would have to communicate the data from the afterworld, for one thing).

The experimental section notes several things that the careless researcher might not have thought about. For one thing, you don't want to make more than a 5% solution in nonpolar solvents. Anything higher and you run the risk of having the pure stuff suddenly come out of solution and oil out on the bottom of the flask, and you certainly don't want that. You also don't want to make a solution in anything that's significantly more volatile than the azide, because then the solvent can evaporate on you, making a more concentrated stock below, and you don't want that, either. Finally, you don't want to put any of these solutions in the freezer - a particularly timely warning, since that's one of the first things many people might be tempted to do - because that'll also concentrate the azide as the solvent freezes. And you don't want that. Do you?

Actually, the careless researcher shouldn't even work with cyanogen azide, or anything like it, but you never can tell what fools will get up to. The compound