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DBL%20Hendrix%20small.png College chemistry, 1983

Derek Lowe The 2002 Model

Dbl%20new%20portrait%20B%26W.png After 10 years of blogging. . .

Derek Lowe, an Arkansan by birth, got his BA from Hendrix College and his PhD in organic chemistry from Duke before spending time in Germany on a Humboldt Fellowship on his post-doc. He's worked for several major pharmaceutical companies since 1989 on drug discovery projects against schizophrenia, Alzheimer's, diabetes, osteoporosis and other diseases. To contact Derek email him directly: derekb.lowe@gmail.com Twitter: Dereklowe

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December 23, 2008

Holiday Break

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Posted by Derek

Posting will be intermittent around here until after January 1st. I'm going to be doing various important tasks at home, such as wrapping presents and making another chocolate pecan pie for folks who didn't get any the last time around. There's also some snow to be shoveled, particularly if I want to get the telescope out during this period of new moon. There's 15 to 20 inches out there on the ground, which is not much of a stable surface for the equatorial platform to sit on, nor do I relish wading through it while hauling the telescope tube itself.

My workplace is very quiet indeed today, I can report, and later on I'll be doing my part to keep it that way. I suspect it's the same across a lot of labs today and for the next few days, and that's a good thing. It's impossible to have good ideas when you're grindstoning away the whole time; you need to clear your head every so often and take a look at what you're actually doing versus what you should be.

This is one of the only times when sleeping late and eating pecan pie come under the heading of "clearing one's head", so I'm going to take full advantage of it. I hope that many of you can do the same!

Comments (19) + TrackBacks (0) | Category: Blog Housekeeping

December 22, 2008

Publish Your Work The Easy Way

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Posted by Derek

I say unkind things about various scientific journals here on occasion. But I have to say that I've never encountered a situation in chemistry that matches the affair of M. S. El Naschie, editor of the Elsevier journal Chaos, Solitons, and Fractals. It's nice to see the editor-in-chief show up with an occasional paper in his own journal - keeping one's hand in and all. But El Naschie has published three hundred and twenty-two papers in the journal since he assumed editorship. He has five in the December issue alone!

The N-Category Cafe, a math blog from the University of Texas, has the full story here. Briefly, El Naschie seems to have been running this journal as his own private kingdom for some time now. While I'm not qualified to referee his works, those who are report that his papers don't make much sense - "undisciplined numerology larded with impressive buzzwords" is one review at the UT site. (That's a phrase I'm going to have to remember for future use; it's bound to come in handy).

Would you like to subscribe to this fine journal, and get the latest updates from El Naschie-land? That'll run you $4520/year. As a library, you'll be getting that as part of a bundle of other presumably more useful journals, so you won't be paying full whack. But still. Why pay anything for a vanity press full of nonsense? (And if there are some real papers in there from other groups, then I pity them for having to appear alongside the gibberish).

Elsevier seems to have finally caught on, after many recent protests. The journal's home page now states:

The Founding Editor for Chaos, Solitons and Fractals Dr El Naschie will retire as Editor-in-Chief. This will be announced in the first issue of 2009. The publisher will work with the editorial board and other advisors to identify a new editor, as well as reviewing the aims and scope of the journal, as well as the editorial policies and submission arrangements.

I'll bet they will. What's puzzling is why this took so long - isn't anyone at Elsevier paying attention? And why did it take some math bloggers to get things rolling - where has everyone else been in the field all this time? Just rolling their eyes and chucking the issues into the circular file, apparently. As I say, I don't know of anything close to this in chemistry - if anyone has info to the contrary, let's get on it ourselves. . .

Comments (44) + TrackBacks (0) | Category: The Scientific Literature

December 19, 2008

My Compound Goes Where the Wild Goose Goes

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Posted by Derek

A colleague and I got to talking yesterday about something that I'm sure many chemists have noticed. Have you ever chased down some reaction or compound in the literature, only to find yourself wild-goosing back to some obscure journal that no one has ever read - just because no one can be bothered to publish a modern procedure?

Here's how that typically works. You run a SciFinder search on Molecular Structure X. A list with a dozen references comes up. There's a Tet. Lett. from 2002, but what are the chances it'll have any spectral data (or anything useful at all?) Ah, there's one from Tetrahedron in 1995, that should do. So you look over the PDF, search for your compound. . .there it is, number 17. Now to the experimental. . .and you find in the first paragraph that "Compound 17 was prepared according to a published procedure", footnote thirty-eight. And the footnote is to. . .ay, it's to a Chem. Ber. paper from 1932. Ausgezeichnet!

Oh-kay. Back to that SciFinder reference list. How about that Tet. Lett. paper? Nope, on inspection, it turns out to reference the 1995 paper you just looked at. What else? There's a JOC from 1984, let's try that. Good ol' JOC, solid stuff. Well, digging up that PDF, you find that it refers to a 1980 paper from the same group from Synthesis. Hrm. So you chase that one down, there it is, compound 9, and the experimental for it is. . .footnoted to the 1932 paper. Again.

And that's how it goes. Like as not, you can go through the whole list and find that it's made of tissue paper where your compound of interest is concerned. The whole presence of the compound in the literature is, in the end, based on some obscure German university's report from the last days of the Weimar Republic. What's irritating is that while those 1932 folks clearly must have made the compound, it's not always easy to get those papers immediately. And chemistry has, in fact, changed a bit since those days. Papers from that era rely on distillation and crystallization: there are no chromatographic purifications, because there was (by our standards) no such thing as chromatrography. Spectral data? Hah! UV/Vis was cutting edge back then. You'll get a melting point, an adjective-laden description of the appearance of the crystals, and maybe even a note about how the stuff tastes. Great.

You know that the people who re-made the stuff during the last 25 years didn't steam-distill their product or fractionally crystallize it from some mixture of benzene and carbon disulfide or whatever. They ran a quick column and they took an NMR. So why can't they publish that data? The only reason I can usually see is laziness. Why bother? It's a known compound; just reference it and get that manuscript out the door. . .

Comments (27) + TrackBacks (0) | Category: The Scientific Literature

December 18, 2008

When Placebos Were All There Were

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Posted by Derek

Yesterday's discussion of how to deal with various forms of pseudoscientific hoo-hah naturally brought up several mentions of the placebo effect. And that prompts me to bring in the late Lewis Thomas's The Youngest Science, his memoir of a life in medicine. We should never forget that there was a time, not all that long ago, when drug therapy was almost all placebos. Here's a description of the way Thomas's father practiced in the 1920s:

Nevertheless, despite his skepticism, he carried his prescription pad everywhere and wrote voluminous prescriptions for all his patients. TThese were fantastic formulations, containing five or six vegetable ingredients, each one requiring careful measuring and weighing by the druggist, who pounded the powder, dissolved it in alcohol, and bottled it with a label giving only the patient's name, the date, and the instructions about dosage. The contents were a deep mystery, and intended to be a mystery. The prescriptions were always written in Latin, to heighten the mystery. The purpose of this kind of therapy was essentially reassurance. . .They were placebos, and they had been the principle mainstay of medicine, the sole technology, for so long a time - millennia - that they had the incantatory power of religious ritual. My father had little faith in the effectiveness of any of them, but he used them daily in practice. They were expected by his patients; a doctor who did not provide such prescriptions would soon have no practice at all. . .

That's the world as it was. Thomas later recounts the profound shock he experienced as an intern when sulfanilamide was introduced: patients given up for dead got up out of their hospital beds and asked for something to eat. It was then, he says, that he realized that the medical profession he was entering might be turning into something different from what his father knew.

We should never forget: it's our job to make our children look back on today's medicines with the same mixture of pity and alarm. To cure disease, stop the damage, make people given up for dead stand up and walk out of the room to see their families. Things aren't going very well for us now in this business, because these are all very hard things to do, and the amount of time and money needed to do them is nearly unbearable. But not quite. We can see that such things are possible, and it's up to us to figure out how to make them real.

Comments (17) + TrackBacks (0) | Category: Drug Industry History

December 17, 2008

Awkward Conversations

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Posted by Derek

We need a lighter topic today, and I’ve got one appropriate to the season, since many people will be having parties and family get-togethers over the next couple of weeks. And although some of these will be full of scientists, there are others where you might be the lone representative from the world of chemistry, biology, or medicine. That can be a good thing – or not so good, depending on how the conversation turns. A reader e-mailed me an account of a recent encounter with a relative who assured him of the benefits of foot-bath detoxification to cure what ails you. As you'd imagine, he didn't quite sign on to that idea, and the discussion went through a few rocky rapids.

I know that this sort of thing has happened to me several times. I’ve had to deal with the topics of how no, it’s not a conspiracy of the drug companies to make vitamin-based therapies illegal – and how yes, I have been working for X number of years in the drug industry without discovering a single thing that’s on the market, and how that’s statistically rather likely. And I’ve explained how it’s hard to come up with a cure for Alzheimer’s when you don’t even know what causes Alzheimer’s, which argument generally meets with agreement. But that reasonable discussion gets canceled out by plenty of others.

Dealing with the crazier propositions takes some real tact. I’m a pretty even-keeled guy, so I generally take a calm approach, just telling them how it is for me after X years of experience in the drug industry. I've found it's harder for people to spout craziness when there's some reasonable person sitting across the table from them who makes a living on the opposite side of their beliefs. And, truth be told, many of the wilder beliefs in the health field aren't necessarily all that strongly held. Most of them don't stand up to much scrutiny (and contradict each other, to boot), and I've found that people pick up and discard them with relative ease.

But you do run into passionate believers now and then. I'd be interested in hearing from people how they've dealt with conversations like this. My usual progression goes something like:

1. That's interesting - where did you hear about this?
2. No, it's true, I really have been working on those diseases for years now. As far as I can tell, they're pretty hard to deal with.
3. Gosh, that anecdotal evidence sure does sound convincing. Pity the FDA won't let us use any of that where I work. Those nutritional supplement manufacturers sure have it easy since the Hatch-Waxman act, don't they?
4. Hmm, since Fact X seems to be true about Disease Y, based on all that I know about the subject, how do these fit together?
5. Well, you know, the laws of physics/chemistry/math that I learned don't seem to cover that particular effect - have they added some recently?
5. No, I think that if there were any conspiracy that big, I probably would have noticed it at some point. Unless you're suggesting that I'm part of the cover-up?
6. Actually, people in the drug industry die from Disease Y, too. You'd think that if we were sitting on the cure for it, we'd have some sort of employee program or something. . .

Comments (30) + TrackBacks (0) | Category: General Scientific News

December 16, 2008

Layoffs. More Layoffs.

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Posted by Derek

I’m told by several people that today Bristol-Myers Squibb is announcing layoffs in research (and perhaps other areas). I don’t know how extensive these are, or how they’re spread across the New Jersey and Connecticut sites. What I do know is that accounting practices make these things especially rough, since a disproportionate number of such cuts take place before year’s end, which doesn’t do much for anyone’s holiday season. (Of course, I suppose it could be even worse – you could be working for Pfizer, and spend the holidays not knowing if your job was going to be there in January or not). In a smaller but deeper cutback, I also note that Entremed, a company that’s been struggling to survive ever since its turn in the spotlight with Judah Folkman’s anti-angiogenic peptides, has announced that sixty per cent of its employees will be let go. Since that includes the CEO and CFO, you have to conclude that the situation there is not good.

Having been through the layoff process myself, I know what the people involved are going through, and I wish them every hope of landing new positions. If anyone out there knows of companies that are hiring now in research, or even planning to, I’d be glad to list such in a separate post in order to provide some leads.

One other related item: I’ve heard from Linda Raber at C&E News who’s working on a "Careers in Pharma" story for them, and wants to write about all the chemistry layoffs this year. She’d like to hear from people who are willing to be quoted on what things have been like. (Update: you don't have to be identified - see the comments section for contact info!) I was quoted in a similar story after the Wonder Drug Factory layoffs, actually; this sort of piece is turning into more of a perennial than anyone would like.

Comments (53) + TrackBacks (0) | Category: Business and Markets | Current Events

December 15, 2008

Insider Trading in Drug Stocks? Not Unknown. . .

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Posted by Derek

With all the financial scandals going on these days (really, a multibillion-dollar Ponzi scheme run by the former head of NASDAQ?), it’s worth asking how often such shady dealing goes on with the stocks of drug companies. From what I can see, it does happen, but it’s certainly not endemic.

The first thing that comes to mind is insider trading. Since many companies see their stock move abruptly on the single news items pertaining to clinical trials results, regulatory actions, adverse events, and so on, front-running is always going to be a problem. And I’m sure that it goes on, but I also know that companies put a lot of effort into trying to keep it from happening. For clinical trial results, that means that such information is strictly need-to-know, and believe me, not that many people need to know. Most companies have a rather short list of people who see such numbers before a public release, which makes tracking down suspicious trades a bit too easy for comfort, if you’re inclined to reach for the easy money. I’m certainly not on any such list myself, and never have been.

There are other kinds of material information, but it’s still rare for anything that goes on in my end of the industry to affect the stock price. We’re just too far from the clinic and from the FDA to make that much of a difference. But in any case, I agree with a definition of “material information” that I once heard: if it makes you think about trading the company’s stock, and it’s not in a press release already, it’s material information. And you act on it at your peril.

But that doesn’t mean that people don’t act. Sam Waksal of Imclone is merely the most famous executive to place a phone call to his broker at an inopportune time. The chief legal counsel over at Biogen Idec got in hot water a couple of years ago about a suspicious options trade around the time of the bad news about the company’s Tysabri. (The case was settled with the SEC, with no language about wrongdoing involved - there was still some reasonable doubt about the timing of the trade, although it would have been far more prudent to not have made it). A few years before that, the chief attorney at Vertex got into trouble with another ill-advised trade of his own company's stock. And there are others, naturally.

Then there's the problem with theoretically-embargoed information from the big clinical meetings like ASCO. In recent years, it's become clear that this stuff is leaking out in one form or another, because interesting trading patterns become evident in the run-up to the meetings themselves. I think that sending out an abstract book while trying to keep the lid on them is probably futile. Of course, in many cases the real stock-moving news in such cases doesn't come from anything in the abstract book, but from the information in the presentations themselves, which is all later-breaking stuff added long after the abstract submission deadline. So you could argue that people trading on the pre-meeting stuff are still kidding themselves. . .

The closest I've ever come to this sort of thing myself was some years ago. A colleague attending a clinically-oriented meeting in a particular medical specialty called some of us back at our company to say that an anticipated series of posters and talks from another company didn't look like it was going to materialize. No one from that organization was putting anything up for the poster session. We guessed that there was some last-minute problem with their compound - and so it proved in a press release the next morning.

It occurred to me during that afternoon that a stock or options trade could well be profitable, but I didn't go through with it. It would have been profitable (especially the options, naturally), but in the end I didn't quite have the nerve. I still don't think that it would have been illegal, but I didn't like the idea of explaining actions of mine in those terms. "Not illegal as far as I know" isn't exactly the rock on which one wishes to make one's stand, you know?

Comments (10) + TrackBacks (0) | Category: Business and Markets | The Dark Side

December 12, 2008

The Worst Biotech CEO?

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Posted by Derek

I'm pleased to note that Adam Feuerstein over at TheStreet.com has announced his first-ever "Worst Biotech CEO" award. In what was surely a contested field, he's named Elan's Kelly Martin as the winner. I was pulling for Ariad's Harvey Berger, who seems to have come close. Well, there's always next year - and yes, I do need to update the Ariad story soon.

Martin's win is a result of the troubles with the anti-Alzheimer's antibody bapineuzumab this year. When pivotal trial results came out back in July, they weren't too exciting. Investors, though, had been very excited indeed, and Elan's stock took a terrible beating as a result. According to Feuerstein, Martin's cheerleading for the drug was the reason for this unprofitable disconnect from reality.

He certainly wouldn't be the first CEO to beat the drum for his company's drug, but this kind of thing has a big risk of backfiring. How do investors believe you after they've been burned in this fashion? You don't want to have to depend on fresh crops of people who haven't heard your story yet. Alzheimer's is a tremendously difficult field to make headway in, and everyone who wants to buy into something in it needs to understand that. As an investment, such drugs are worth taking a flier on, but with a clear understanding that the odds are long. I think that Elan (and their partner, Wyeth) deserve credit for going after something as unusual as an immune-based therapy for the disease, but there's no excuse for making people think that it's working if it really isn't.

Anyway, be sure to check out Feuerstein's take, along with the comments on Vanda, Medarex, and other favorites. I hope he keeps this up year after year: there will never be any shortage of contenders.

Comments (7) + TrackBacks (0) | Category: Business and Markets

December 11, 2008

Pfizer's Restructuring Grinds Along

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Posted by Derek

So, Pfizer: it seems as if they’ve been going on about cutting their research staff for months now. Well, its has been months, and the whole thing is turning into a rather bitter joke for people in Groton, from what I can tell. This current wave of restructuring has been rumbling along since back in the summer, and they told people about the layoffs in the fall. How long is all this going to take?

The latest announcement from the higher layers is that the company will announce its plans “sometime in January”. Lee Howard, a reporter at the New London paper The Day, has a copy of a letter from Pfizer’s Rod MacKenzie (head of discovery research worldwide) to employees, saying that because the changes in research are so complex, he won’t be able to communicate them by the end of the year. I’m not sure if the letter includes his greetings for a Merry Christmas and a Happy New Year; maybe that one will arrive in time for Valentine’s Day. Here's the article, the comments to which erupt in a lot of vituperative town-vs-gown New London crossfire.

From what I’m hearing, the coming changes are going to be quite profound in chemistry. Pfizer seems to be dividing its chemists up into people who think up molecules, and people who make them, with no real overlap. You’re probably thinking sure, that’s how the Germans and the Swiss tend to do it, the PhDs in the offices and the BS/MS folks out at the hood. But apparently there are PhDs on the “make the molecules” side in Pfizer’s new scheme, although I think the “design the molecules” side will have no one who isn’t. At any rate, the traditional medicinal chemist, someone who has an idea for a new molecule and then goes out to the lab and makes it, will seemingly have no place at Pfizer. You do one, or you do the other.

And I’ve heard from several sources that major outsourcing will be a big part of the new system as well. The “drug designers” will also be resource managers, spending their time figuring out what compounds and series to ship over to China, and what to have the local groups work on. As readers here well know, I think that outsourcing definitely has its place, but Pfizer seems to be going even further down that road than the rest of the industry – how well that’s going to work is an open question. A lot of the outsourcing work I’ve seen over the years has been. . .OK. Used judiciously, that’s fine, but I don’t know if I’d want to base whole programs on it if I didn’t have to.

I think it’s safe to say that morale and productivity in the labs in Groton must be drooping a bit these days. How could it not be, with everyone waiting for months to see who’s going to be let go, and in this economic climate? I understand that it’s a big organization, and that figuring out what to do is a complicated job. I certainly wouldn’t want it. But the way this is being done has not reflected well on the company’s management and how it treats its employees. But we’ll just have to add this one to the existing lists in both categories. . .

Comments (57) + TrackBacks (0) | Category: Business and Markets | Current Events

December 10, 2008

Floppiness Is Not Your Friend: Who Knew?

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Posted by Derek

There’s a trick that every medicinal chemist learns very early, and continues to apply every time its feasible: take two parts of your compound, and tie them together into a ring.

The reason that works so well may not be immediately obvious if you’re not a medicinal chemist, so let me expand on them a bit. The first thing to know is that this method tends to work either really well or not at all – it’s a “death or glory” move. And that gives you a clue as to what’s going on. The idea is that the rotatable bonds in your molecule are, under normal conditions, doing just that: rotating. Any molecule the size of a normal drug has all kinds of possible shapes and rotational isomers, and room temperature is an energetic enough environment to populate a lot of them.

But there’s only one of them that’s the best for fitting into your drug target, most likely. So what are the odds? As your molecule approaches its binding pocket, there’s a complicated energetic dance going on. Different parts of your drug candidate will start interacting with the target (usually a protein), and that starts to tie down all that floppy rotation. The question is, does the gain resulting from these interactions cancel out the energetic price that has to be paid for them? Is there a pathway that leads to a favorable tight-binding situation, or is your molecule going to approach, flop around a bit, and dance away?

Several things are at work during that shall-we-dance period. The different conformations of your compound vary in energy, depending on how much its parts are starting to bang into each other, and how much you’re asking the bonds to twist around. The closer that desired drug-binding shape is to the shape your molecule wants to be in anyway, the better off you are, from that perspective. So tying back the molecule and making a ring in the structure does one thing immediately: it cuts down on the range of conformations it can take, in the same way that tying a rope between your ankles cuts down on your ability to dance. You’ve handcuffed your molecule, which would probably be cruel if they were sentient, but then, a lot of organic chemistry would be pretty unspeakable if molecules had feelings.

That’s why this method tends to be either a big winner or a big loser. If the preferred binding mode of your compound is close to the shape it takes when you tie it down, then you’ve suddenly zeroed in on just the thing you want, and the binding affinity is going to take a big leap. But if it’s not, well, you’ve now probably made it impossible for the thing to adopt the conformation it needs, and the binding affinity is going to take a big leap over a cliff.

There’s another effect to reducing the flexibility of your compound, and that has to do with entropy. All that favorable-interaction business is one component of the energy involved, namely the enthalpy, but entropy is the other. Loosely speaking, the more disordered a system, the higher its entropy. A floppy molecule, when it binds to a drug target, has to settle down into a much tighter fit, and entropically, that’s unfavorable. Energetically, you’re paying to do that. But if your molecule is already much less flexible, there’s not much of a toll as it fits into the pocket. If loss-of-floppiness is a bad thing, then don’t start out with so much of it.

So, how much do I and my medicinal chemistry colleagues think about this stuff, day to day? A fair amount, but there are parts of it that we probably don’t pay enough attention to. Entropy gets less respect from us than it deserves, I think. It’s easy to imagine molecules bumping into each other, sticking and unsticking, but the more nebulous change-in-disorder part of the equation is just as important. And it doesn’t just apply to our drug molecules – proteins get less disordered as they bind those molecules (or more disordered, in some cases), and those entropic changes can mean a lot, too.

I also mentioned molecules finding a pathway to binding, and that’s something that we don’t think about as much, either. We probably make things all the time that would be potent binders, if they just could get past some energetic hump and wedge themselves into place. But there are no crowbars available; our drug candidates have to be able to work their way in on their own. The can’t-get-there-from-here cases come back from the assays as inactive. The tendency is to imagine these in the binding site already, and to try to think of what could be going wrong in there – but it may be that they’d be fine, but that their structures won’t allow them to come in for a landing.

Picturing this accurately is very hard indeed. We have enough trouble with good representations of static pictures of our molecules bound to their targets, so making a movie of the process is a whole different story. Each frame is on a femtosecond scale – molecules flip around rather quickly – and every frame would have to be computed accurately (drug structure, protein structure, and the energetics of the whole system) for the resulting video clip to make sense. It’s been done, but not all that often, and we’re not good at it.

Comments (13) + TrackBacks (0) | Category: In Silico | Pharma 101

December 9, 2008

Goldman Sachs: A New Drug Research Model?

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Posted by Derek

Now, here’s an odd item from the Financial Times (registration required):

Goldman Sachs is in talks to provide hundreds of millions of dollars of funding to a large pharmaceutical company, in the first evidence of a new business model for the sector that will see financing shifted away from funding companies and towards targeted co-development of specific medicines. . .

. . .(The model involves) a different approach, creating a "research pool" into which pharma companies would place a range of experimental drugs in a single therapeutic area in early-stage phase 1 and 2 trials, where their specialists would work alongside external experts including scientists, chemists and clinical research organizations.

This was announced at a conference run by the newspaper, so they’re really the only source for information on this. I haven’t been able to find anything from Goldman about it, for example, and the minimal press coverage so far has all pointed back to this article. (Ed Silverman picked it up at Pharmalot, for example).

So one wonders what’s up, because the information that’s given raises more questions than it answers. I presume that the assumption is that since only a few early-stage clinical compounds ever make it, that this gives everyone a chance to share the risk. But which therapeutic area are we talking about here? How are things apportioned when one compound makes it through? And what if more than one does? And where are these external experts coming from, and who pays them?

This could be very interesting, because I think that we need to be open to some new research models in the industry. The current one isn’t exactly spewing results these days. But I wish that I knew more about what this proposal involves – anyone out there have any more details that they can share?

Comments (12) + TrackBacks (0) | Category: Business and Markets | Clinical Trials | Drug Development

December 8, 2008

Enhancing the Brain: Here We Go

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Posted by Derek

Depending on what news sources you follow, you may have heard a lot about it already: taking cognition-enhancing drugs to improve normal brain function. An editorial in Nature has just come out in favor of it, so although I wrote about this back in April, it’s time to talk over the issue again.

Let's define what we're talking about first. We really don’t have anything to selectively affect memory or general intelligence per se, but we do know something about how to affect attention span and wakefulness. So right now, cognition enhancement is mostly going to be found via the stimulants used for attention-deficit disorders, along with Cephalon’s Provigil (modafinil) for narcolepsy. These are the drugs of issue.

Nature started off this latest debate on this a few months ago, when they took an informal survey to see how many scientists used these. The results came in as “more than you might think”, although still a decided minority. One got the impression that these were reached for during grant-writing time in academia, for the most part, which would make their usage pattern similar to what you’d find among the student population. My guess is that the number of people using these in industrial research would be far smaller, for several reasons. For one thing, our work moves in different rhythms. As opposed to academia, we rarely have situations where a Big Creative Work has to be produced (or a huge pile of facts memorized) under time pressure. We do have big reports and presentations that come due, of course, but by the time the big ones are due there have been a lot of smaller ones, and the slides and material are largely summaries of those. It’s not to say that many of us couldn’t benefit from some extra attention to our work, it’s just that the opportunities for such aid aren’t as clear-cut.

Any discussion of this topic has to start with the question of how much good such drugs do. I’m willing to stipulate that for situations like the ones I’ve been describing – a need for long, sustained periods of focus and attention to detail – that these compounds do indeed help. They may be more beneficial for some people than for others, but yes, I think that their effect is real. (If anyone has evidence to the contrary, I’d be glad to hear it – I should also mention that I have no personal experience to draw on).

And that brings up another question, the second big one that always comes up in such a discussion: is it right to do this sort of thing? Now that’s a tangle, because a value judgment has come into the room. And anyone who wants to take a hard line has to deal with the fact that we already have a legal, well-known, widely used drug for cognitive enhancement: caffeine. If that doesn’t increase wakefulness, I’d like to know what does.

The comparison with steroid use in sports will also come up, although I regard that one as partially a red herring. The whole point of athletic competition is different from the point of achievement in the arts and sciences. All sports are essentially artificial constructs that we agree on rules for, and doping makes people worried and/or furious that these rules are being bent. Science, on the other hand, is the real world. If Barry Bonds did indeed break home run records with chemical aid – personally, I think he did – then a lot of people (including me) have a problem with that. But if someone comes up with, say, a proof of the Riemann Hypothesis with the use of modafinil and methylphenidate, well. . .a proof is a proof.

But there is a competitive aspect that the sports analogy does bear on: several junior faculty may all be vying for tenure at the same time, for example. If they’re all roughly equal in ability, does the appointment end up going to the one who uses pharmacological help most effectively? That’s where the same uneasy feeling starts to set in. It’s when you look at head-to-head, human-to-human cases that the arguing really gets going.

We’re going to have more and more of this to deal with in the future. I don’t expect it any time soon, but we’ll eventually be able to do more for memory – and, for all I know, for higher cognition. There are too many therapeutic reasons to investigate such things, and too many reasons for any useful drugs not to quickly escape to the population that doesn’t necessarily have anything wrong with it.

All of these issues are addressed by the authors of the latest Nature commentary, naturally. For example:

"Consider an examination that only a certain percentage can pass. It would seem unfair to allow some, but not all, students to use cognitive enhancements, akin to allowing some students taking a maths test to use a calculator while others must go without. (Mitigating such unfairness may raise issues of indirect coercion, as discussed above.) Of course, in some ways, this kind of unfairness already exists. Differences in education, including private tutoring, preparatory courses and other enriching experiences give some students an advantage over others.

Whether the cognitive enhancement is substantially unfair may depend on its availability, and on the nature of its effects. Does it actually improve learning or does it just temporarily boost exam performance? In the latter case it would prevent a valid measure of the competency of the examinee and would therefore be unfair. But if it were to enhance long-term learning, we may be more willing to accept enhancement. After all, unlike athletic competitions, in many cases cognitive enhancements are not zero-sum games. Cognitive enhancement, unlike enhancement for sports competitions, could lead to substantive improvements in the world."

The editorial comes down to several main points: that we need more solid data on the benefits and risks of such drugs for normal individuals, that competent adults should have to option to use them, and that policies should be worked out to deal with issues of fairness, coercion, and the like.

My own thoughts on this are deeply confused and divided. That’s partly because I’m a weirdo: I don’t drink alcohol, and in fact, I don’t even drink coffee. That goes back to what I’d have to classify as a deep reluctance to mess with the way my brain works through chemical means, a trait that was already well in place by the time I was a teenager, but which was only reinforced as I learned more and more biochemistry. So on one level, I have to think that we really don’t know enough about how the existing cognitive enhancing drugs work, let alone what we’ll know about future ones, and that alone would keep me away from them.

But I can come up with plenty of thought experiments that shake me up: imagine that the risks are better known, and that they're as much as, say, caffeine (but with more benefits). What then? What if such things turn out, many years in the future, to be necessary to work at any reasonably high level in science, since everyone else will be taking them, too? Is part of my problem with drugs that alter brain function a streak of Puritanism - would I feel better about using such things if I knew that they were guaranteed not to be enjoyable? And so on. . .I have to confess, I found such issues a lot easier to deal with inside the confines of old science fiction stories.

Comments (20) + TrackBacks (0) | Category: General Scientific News | The Central Nervous System

December 5, 2008

Squinting At The Pictures, The Modern Way

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Posted by Derek

Fellow chemists, let’s address a housekeeping problem. I know that not all of us are thrilled at all times with the American Chemical Society, but I think that we can agree that the journals it runs are (for the most part) a valuable resource.

And in these days of modern times, as the Firesign Theatre used to say, the presence of such journals on the internet is crucial. As many of you know, the ACS recently revamped the web pages for its journals, adding a number of new functions. Unfortunately, they seem to have taken away some at the same time.

Initially, on too many of journal sites, the graphical abstract was presented at a default size of “itsy bitsy”. If you wanted to browse the ASAP in-press articles, you had to squint at tiny, fuzzy blobs to see what the authors of each article wanted you to know about it. And that’s clearly not what a graphical abstract is for, is it? I'm relieved to see that this seems to have improved in the last few days.

But I'm not sure when the change took place, because I hardly ever visit the front doors of the ACS journals I read. That’s because I, like many other scientists, follow these things through RSS feeds. (I use Google Reader myself – if anyone’s just setting up an RSS reader and would like my OPML file, just e-mail me and I’ll send it along and save you some time).

And what does the RSS feed look like now? Well, for several days, there were no graphical abstracts at all, which made the ACS feeds look just as ugly and nonfunctional as the Elsevier ones. Way to go! (Isn’t it odd that Tet Letters, the journal that pioneered the whole idea of a graphical abstract in chemistry, doesn’t include its graphics in its RSS stream? I don’t get any, at any rate). Which reminds me - if you don't care for the Wiley feeds, either, specifically Angewandte Chemie's, you can get a better version of that one here.

I wrote the ACS support people and complained about the problem, and was told that they were fixing things. Well, their idea of a fix is apparently to include the tiny, blurry graphic in the feed – those have started showing up this week, and an irritatingly useless sight they are. This is one of those examples of taking something that was perfectly useful before – the RSS feeds they way they were last month – and improving them into junk. The ACS pages will be down again on Sunday, presumably for more fine-tuning. We'll see if the feeds return to functionality next week. If they don't. . .well, please consider adding your voice to the chorus asking that they do. Thanks!

Comments (19) + TrackBacks (0) | Category: The Scientific Literature

December 4, 2008

Curse Of the Lost Compounds

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Posted by Derek

There are some groups of compounds that seem to have a curse on them. They show up in drug screening, they have activity that’s often too good to ignore, but hardly anyone can manage to turn one of them into a drug.

Trifluoromethyl ketones are one example of this. They’re classic inhibitors of proteases, especially serine proteases, and of other enzymes that depend on a serine in their active site. That’s because that ketone really isn’t much of a ketone – the fluorines make the carbon rather unhappy when it’s in that state, electron-poor and ready to pick up a nucleophile and go tetrahedral again. Trifluoromethyl ketones are generally seen in their hydrated state, unless you take care to dry them out, and they’ll work an active-site serine OH into their scheme as well. So you end up with a covalent inhibitor, but a reversible one – the activity comes on slowly, and the compound comes off slowly, too. That trick can work with cysteine nucleophiles, and the hydrate form is also known to coordinate with active-site zinc atoms – so it’s no surprise that the enzyme inhibition literature on these things is mighty extensive: proteases, lipases, esterases, deacetylases, the list goes on for a while.

But although several of these have gone into the clinic over the years, I can’t think of one that’s make it all the way to the market (I’d be glad to hear of any that I’ve overlooked). The best guess is that this isn’t the fault of the functional group, but of the targets it’s been applied to. Some of these enzymes just haven’t panned out, so perhaps the trifluoromethyl ketone awaits its day in the sun.

Another group of this sort is the hydroxamic acid. Its strength is its coordination to zinc atoms, so you see it all over the place in the metallaloprotease literature, and in other zinc-y fields like histone deacetylases. And in vitro, it hardly has a peer. I’ve seen list after list in the literature comparing various zinc-binding head groups, and likely as not, the hydroxamic acid sets the standard every time.

But the reason you see those lists is that people are trying to find something that’ll work other than a hydroxamic acid. There are numerous complaints, ranging from “hydroxylamine is explosive on large scale, you know” and “they’re a pain to make reproducibly” through “they have ugly PK in the animal models” all the way up to “they’re toxic” and “how many of them have ever made it through the clinic?”. How much merit each of these have can be debated, but all together they make an unpleasant picture.

In this case, though, I do know of one that’s made it - SAHA (Zolinza, vorinostat). That one came out of a long-term academic project involving Paul Marks at Sloan-Kettering and Ron Breslow's lab at Columbia, and is one of the not-so-numerous examples of drugs that have made it from the university to the marketplace. Merck signed up to do the clinical and regulatory lifting on this one, and it's now marketed for cutaneous T-cell lymphoma.

So it is possible to get a hydroxamic acid through. "Well, yeah," say the voices, "for cancer, sure. Home of the world's only boronic acid-containing drug. Home, if you really want to get down to it, of nitrogen mustards and God knows what else. Cancer." And it's true that the standards are a bit more relaxed there. I wouldn't necessarily want to give someone a hydoxamic acid every day for the rest of their life, true - the things coordinate iron, for one thing, which isn't always good. But there are other fields where short-term therapy makes sense, and we probably haven't seen the last of this functional group, either.

Comments (22) + TrackBacks (0) | Category: Cancer | Drug Development | Drug Industry History

December 3, 2008

Roche Stalls For Time

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Posted by Derek

Remember back earlier this year, when the temperatures were high, the Dow was at 11,000, and Roche announced that they wanted to buy the rest of Genentech. So how’s that working out?

Not all that well, as far as can be told from the outside. This would take around 45 billion dollars, and 45 billion dollars is a sum that’s increasingly hard to borrow these days. According to Reuters, the prospects for Roche putting together a syndicated loan for that amount are “becoming increasingly remote”. I can believe it. That would surely be the largest deal going at the moment, and given the state of the credit markets, the terms would probably curl your hair if they did manage to float such a beast. And who’s willing to, even if they have that kind of capital sitting around?

For its part, Roche has been telling everyone that they’re still committed to buying Genentech, and that they’re completely confident of getting the financing together. Of course, they’ve been saying that since July, basically word for word, and as the months go on those repeated statements of confidence start to have the opposite effect. So if Roche really is committed and so on, what are they going to have to do?

Reach in and dig out more equity and cash, most likely. What else? Apparently the company is trying to avoid doing that, and they’re willing to leave things hanging until the situation improves. But if you can predict when people are going to be in the mood to lend that kind of money, well, you should be out there making a fortune on the Street with such insights. (I would be!) And if anyone tells you that they have the macroeconomic situation figured out for the next few months, ask them if they went short on oil futures back in the summer. You’d think that anyone with any kind of magic touch would have known enough to do that.

One consequence of all this is that people at Genentech have been living in a cloud of uncertainty for months now, and will stay there for the foreseeable future. That can’t be helping morale or productivity. And if there are any places for people to go, it’s also giving them plenty of time to find them. No, Roche’s timing, in retrospect, looks perfectly awful. When (and if) they finally get around to buying Genentech, what, exactly, will they have bought?

Update: a Genentech VP says that all this has had no impact on morale, actually. You can take that as you wish. . .as for me, I'd find that extraordinary, if it were true.

Comments (14) + TrackBacks (0) | Category: Business and Markets

December 2, 2008

Torcetrapib: What Was the Problem? And Does It Matter?

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Posted by Derek

Ever since the catastrophic failure of Pfizer's HDL-raising CETP inhibitor torcetrapib in late 2006, everyone involved has wondered just what the problem was. There was a definitely higher cardiovascular-linked death rate in the drug-treatment group as opposed to placebo - which led to the screeching halt in Phase III, as well it might - but why? Is there something unexpectedly bad about raising HDL? Or just in raising it by inhibiting the CETP enzyme, which might well provide a different lipoprotein profile than other high-HDL ideas? Was it perhaps an off-target effect of the drug that had nothing to do with its mechanism? And for any of these possibilities, is there the possibility of a biomarker that could warn of approaching trouble?

There are now two analyses of clinical data that may shed some light on these questions (thanks to Heartwire for details and follow-up). The first, a new analysis from Holland of the RADIANCE trial data, shows an electrolyte imbalance (low potassium and higher sodium) in the treatment group. Measuring carotid wall thickness, they found no correlation between the degree of HDL elevation and progress of disease, which is disturbing. The only correlation was with lower LDL levels, and the authors point out that torcetrapib has unappreciated LDL-lowering activity. (Of course, there are easier and more proven ways to do that!)

The second, the ultrasound-monitored trial called ILLUSTRATE led by the Cleveland Clinic, actually did show a correlation between HDL levels and disease progression, as measured by PAV (per cent atheroma volume). This paper concludes that the drug did perform mechanistically, but that needs some qualification. Overall, there was no real significant change in PAV, but looking more closely, the individual changes did seem to correlate with the amount of HDL elevation each group of patients achieved. Only the very highest-responding group showed any regression, though.

Interestingly, this study also showed the same sort of electrolyte imbalance, and both teams seem to agree that torcetrapib is showing off-target mineralcorticoid effects. Steve Nissen of the Cleveland group is more optimistic (a phrase one doesn't get to write every day). He thinks that a CETP inhibitor that doesn't hit the adrenals might still find a place - but I have to say, looking over the data, that it sure won't be the place that the companies involved were hoping for. Instead of being world-conquering cardiovascular wonder drugs, perhaps the best this class of compounds can hope for is a niche, perhaps alongside statin therapy. I just don't see how this level of efficacy translates into something all that useful.

But we'll see. Merck's anacetrapib is still going along. The data we have so far suggest that the compound raises HDL without effects on blood pressure, as opposed to torcetrapib. So maybe (for whatever reason - blind luck, I'd say) this compound doesn't do anything to the aldosterone pathway. But does it do anything to atherosclerosis? That's the question, and that's what the big money will have to be spent on in Phase III to find out. A comment at the Wall Street Journal's Helath Blog has it right:

Welcome to the challenges of pharmaceutical research. Pharmacogenomic evidence originally led Pfizer to hope that elevating HDL through inhibiting CETP would be beneficial. A biomarker assessment in patients suggests that plaque reduction is associated with the highest HDL elevations. Yet, with torcetrapib, there appears to be a safety biomarker popping up. Are either the efficacy or safety signals really biomarkers of long term clinical outcome? You only need to ante up $800M to run mortality and morbidity trials for 5 or more years. Any investors?

Comments (3) + TrackBacks (0) | Category: Cardiovascular Disease | Clinical Trials | Toxicology

December 1, 2008

Prodrugs: How the Pros Do It?

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Posted by Derek

I’m going to write this morning about a question that actually came up among several of us at the train station this morning. I’m on a route that takes a lot of people into Cambridge, so we have a good proportion of pharma/biotech people on board. And today we got to talking about prodrugs: like 'em or hate 'em?

For those not in the business, a prodrug is a masked form of an active drug, designed to be activated once it’s dosed. That’s generally done by allowing the normal metabolic processes of the body to clip some group off, revealing the real drug. Various esters are the most common prodrugs, since that’s about the easiest group to have fall apart on you. (Enalapril / enalaprilat is a classic example, and aspirin is an even more classic one).

And esters illustrate another point about prodrugs: no one develops them unless they have to, as far as I’m concerned. After all, if your compound works fine in its native form, why get fancy? No, I think you turn to the prodrug strategy when there’s something wrong. Maybe the active form of the drug isn’t well absorbed from the gut, or has too short a half-life in the blood, or doesn’t distribute to the right organs. The differences in these properties between carboxylic acids and their esters can be particularly dramatic.

There are other ways to do it. Some compounds are oxidized by liver enzymes to turn into their active forms, for example. But all of these ideas suffer from several complications, which is why I’ve always regarded them as acts of desperation. For one thing, all these metabolic pathways vary a good deal between species. That’s a problem for any drug development effort, of course, but you’ve doubled those headaches (at least) by working with a prodrug. Now you have to wonder, when you finally get to humans, if the conversion of the initial compound will take place to the same extent, as well as about the clearance of the active drug (and, for that matter, the non-productive clearance of the prodrug molecule itself). For a development group, taking on a prodrug can be like taking on two drugs at the same time.

There have been all sorts of ingenious ideas along these lines over the years. It’s been my impression that delivery methods of this sort have been more popular among academic medicinal chemistry groups than they have in industry, to be honest. There are all sorts of schemes for targeting active substances to particular organs, or for getting them into hard-to-reach areas like the brain through use of exotic prodrug groups. Most of these don’t survive exposure to the real world, but I can’t turn up my nose at them, either, because these are all things that we would like to be able to do in this business. If weird ideas don’t get tried, we’ll never find out if any of them actually work.

And there have been some real successes in the prodrug field, and it’s always an idea that comes up whenever a lead compound series shows some undesirable absorption or excretion. I’ve broached the topic a few times myself on past projects. But every time, we’ve been able to solve the problem by less drastic means – a new formulation, a salt form, or by just plain old going to a different compound in the end. If you can do it by some combination of those, I'd say you're probably better off in the end. (For those who are taking the plunge, you can probably learn about as much as can be learned from the literature here). Here's an even more recent review.

Comments (12) + TrackBacks (0) | Category: Drug Development | Pharmacokinetics