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Here we'll review recent developments in drug discovery and medicine and the IP issues and financial implications they have, along with general thoughts about research. Also likely to make an appearance: occasional digressions into useful topics like which lab reagents smell the worst.

About this author

Derek Lowe mugshot

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.


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IN THE PIPELINE: drug discovery

By Derek Lowe


Thursday, May 29, 2003

More Blood or Less?

An interesting theory has been floated about the efficacy of Genentech's Avastin antibody for cancer. I wrote about this a few days back - since then, the company's stock has been on an extended tear, and the news of their successful trial helped everyone else in the anti-angiogenesis field, too.

But is the drug really shutting down the blood supply to the tumor? Or, as Lee Ellis of M. D. Anderson in Houston theorizes in the invaluable biotech newsletter BioCentury, is it actually increasing it? That's subscription-only (and how, at a minimum of $2000/year,) but Ellis also refers in passing to this idea in this news release from Anderson:

As an example of how difficult it is to test these new drugs, Ellis and other colleagues at M. D. Anderson have found that using an anti-angiogenesis inhibitor may initially increase blood flow to a tumor rather than decrease it. "Ironically, it may reduce leakiness in blood vessels, and allow small vessels to open up," he says.

He seems to suspect that Avastin (and any other drug targeting VEGF/KDR) might work the same way. If that's true, then several interesting things follow. The drugs would not be expected to be effective on their own. They'd work by allowing other chemotherapy agents greater access to the tumor. And only drugs targeting the VEGF system would probably have this effect. Other angiogenesis targets will stand or fall on the standard mechanism (mostly, they've been falling.)

So, if this pans out, the run-up in other biotech stocks in the area may not be justified - at least, not if the main factor was investors thinking "finally, they've got this anti-angiogenesis thing worked out."

It's too early to say if this idea is correct, but it's intruiging. And it should be testable. If Ellis is right, I would think that various imaging agents for NMR, PET and so on would have better access to the tumor tissue (and show less leakage into its surroundings.) Depends on how good your resolution is, but a careful selection of a model system might allow you to see it.

At any rate, expect a barrage of cancer therapy news (Avastin, Erbitux, and more) starting on Saturday. That's when the American Society for Clinical Oncology meeting starts in Chicago. ASCO embargos its presentations, so there's a lot of pent-up demand for data when the speakers get up to the podium. It's one of those get-on-your-cell-phone meetings - the more clinicians there are at one of these hoedowns, the more frantic phone calls get made. At the basic science meetings I tend to attend, there's not so much of a rush. You've got several years to wait. A carrier pigeon would be just as useful as a cell phone.

Actually, for some of the things you hear about, a carrier sloth would fit in just fine. . .


posted at 9:15 pm

Wednesday, May 28, 2003

Where is That Stuff?

I was rooting around several labs today, looking for reagents. Like all large research companies, we have an inventory system that, in theory, lets us track down specific bottles of chemicals from lab to lab. That way, if it's something that you don't have yourself, you can traipse down the hall and get it from one of your neighbors (and don't waste time and money ordering it again.)

In practice, all these systems have some bugs and blind spots. Even right after we've done inventory on the lab, there are still things that we're supposed to have that no on can seem to find (worse, I always remember seeing the stuff, too.) Every lab has their own system of filing things - usually alphabetical, with organic reagents in one area and inorganics (a smaller group) in another. So far, so rational.

But there are birds-of-a-feather chemicals like organolithiums and Grignards that beg to be kept with each other. Then you'd probably want to keep all the isocyanates with their brethren, because when you want one of them (they give you a one-step way to make a urea compound, for the non-chemical folks out there,) you generally want a whole bunch. (Sort of like potato chips, although I'm glad that potato chips don't smell like isocyanates. I wish that the ureas I've made all had the oral absorption properties of potato chips, too, come to think of it. Most of 'em seem to have more in common with polishing grit.) And the sulfonyl chlorides should be together, right? What about a chlorosulfonyl isocyanate, with both functional groups in the same molecule? No system's perfect; it's like proposals for voting schemes.

My lab is infamous. We have the most bottles of different reagents, which is how I like it. But we can only find about 70% of them, on a good day. Most of the storage areas are alphabetical, but chemical names tend to cluster together, so some shelves are a real rat's nest. Take "C" - there come all the things that start with "chloro," mixed in with the ones that start with "cyclo-" And the "D" shelf makes that one look good, because it's full of "Di-" everything. There's a separate shelf of primary and secondary amines, and the sulfonyl chlorides are all together, and we each have our private stockpiles over at our lab benches, and then there's that overstuffed fridge. . .

Ah, the lab fridge. If you life an evil life, prepare to come back as one of these. Chemistry fridges reek, by tradition and necessity. Sometimes it's an acrylate tang, which never seems to go away, or some fishy amine that lingers no matter what you do. A musty isocyanate or acid chloride whiff tends to hang around, too. None of them are very appealing.

Which reminds me of a safety meeting at a former company of mine. We were required to attend "refrigerator safety" training (eye-rolling, groans.) The speaker, at one point, earnestly advised us that we were not supposed to keep food in our laboratory refrigerators. This priceless wisdom marked him as a complete loser, of course, since he was clearly unaware that lab fridges smell like the mouth of Hell. If for some insane reason I found a sandwich in one, the only way I'd eat it would be at gunpoint.

"And that goes for your freezers, too!" he went on to say. Came a loud voice from a labmate sitting behind me: "Damn! No more Otter Pops!"


posted at 8:54 pm

Tuesday, May 27, 2003

More on Cancer and Old Age

While I'm on the subject, the latest Nature Reviews: Cancer has an excellent review article entitled "Cancer and Ageing: Rival Demons?" It's by Judith Campisi at Lawrence Berkeley, and it goes into just the sorts of issues I brought up yesterday.

It does so at length and in detail, so I'm not going to attempt to summarize the article, which itself is a summary of well over a hundred references. Anyone looking for a one-stop treatment of the subject should read it. One of the key points it covers, though, is the role of the p53 protein, which is about as famous as a transcription factor ever gets.

p53 is the key player in one of the major tumor-suppression mechanisms of higher organisms. I wouldn't even want to guess how many papers have referred to it over the years. It's involved in the "gatekeeper" role that leads to apoptosis, not the tumor-prevention side of things (DNA repair, free radical traps, and so on.) Three lines of mice have been created that have elevated p53 activity, and all three of them have lower rates of cancer, as you'd expect. But two of the three have shorter lifespans (the third is about normal; it certainly isn't longer.)

That's an interesting result, and not just for being the flip side of the effect I spoke of yesterday (where possible means to increase lifespan might lead to increased cancer.) Cancer is supposed to be one of the main causes of death in aged mice, just as in humans. So why wouldn't a lower cancer rate lead to a longer lifespan? As it turns out, the two lines with shorter lives also show evidence of premature aging.

So, is that the choice we have? Cancer or old age - and if you hang in there long enough, you're welcome to both? It could well be, although it pains me to say it. But there are still some escape clauses. The three lines of p53-enhanced mice regulate the protein in a different way - in the two shorter-lived strains, the protein is basically being produced full-on, all the time. The line with a normal lifespan (and, as far as is known at the moment, no premature aging) seems to be regulating it p53 production more normally. It produces the protein at the right times, just more of it each time than usual. That may turn out to be a key; there's a lot about the regulation of such proteins that's still obscure, despite the years of work on them.

And, if it came to that, I think that it would be worth settling for a normal lifespan with a much lower chance of cancer. That's not such a bad deal - it only looks like a compromise when you consider what might have been. But it's too early to use that verb form, because we're only just beginning to get our hands on the controls here. There are still plenty of possibilities for longer lifespan, and plenty of ways to evade what looks like the tumorgenesis tradeoff. It's going to take time, effort, luck - and for the first person to try it, it's going to take a tremendous amount of nerve. To say the least. . .


posted at 9:42 pm

Monday, May 26, 2003

Life and Death - Literally

I've written on and off about the various genes that have been found to influence lifespan in simple organisms (yeast, C. elegans roundworms, fruit flies and so on.) These studies have been working their way up into the small mammals (on their way to humans?), and now there's another candidate which may help to explain a lot of what's going on. The problem is, if this is the answer, we may not like it very much.

It's been known for some time that straight caloric restriction lengthens life span in many animal species. The studies are up to dogs and primates, which are rather long-lived, and a number of people are taking a flyer on the idea as well. It's also well established that the gene called SIR2 in yeast and roundworms has a big effect on lifespan. An extra copy of the gene lengthens life; deletion shortens it. And if the organisms don't have the SIR2 gene, caloric restriction has no effect at all, so it may well be a more fundamental player.

Now another layer seems to have been peeled back. The SIR2 gene's protein is a histone deactylase, which is suggestive. Those are required to unwind DNA from the histone proteins in the nucleus so it can be transcribed, which is a complex process that's getting a lot of attention these days. The enzyme is dependent on NAD+, which is no great distinction by itself (the NAD - NADH redox pair is a chemical coupling that runs a lot of enzymatic reactions.) Caloric restriction doesn't lead to increased amounts of the enzyme itself, so the current study (from a team at Harvard, led by David Sinclair, and published in the May 8 issue of Nature) assumed that the enzyme's level of activity must be changing.

The enzyme's reaction produced nicotinamide as a by-product, which turns around and inhibits the enzyme from further activity. (That sort of feedback inhibition is a common biochemical trick, as my readers in the field well know.) The Harvard team picked up on another enzyme, PNC1, which clears out nicotinamide (by converting it to nicotinic acid, which can, in fact, be cycled around to make more NAD+.) The idea was to remove the product inhibition of nicotinamide, and perhaps to simultaneously increase the amount of the NAD+ that the enzyme needs to run - simultaneously taking the foot off the brake and stepping on the gas, if you will. (As it turns out, it's probably just the first mechanism that's important, due to a number of experimental variations that I'm not summarizing here. NAD+ has a lot of other places it can go, for one thing, while nicotinamide may be a more specific regulator.)

Yeast with the PNC1-forming gene deleted showed the same effects as those that had their SIR2 deleted. They had shorter lifespans, and caloric restriction didn't help them - so far, so good. Then the research team shoveled five extra copies of the gene in, and they found that, under normal conditions, the yeast lived a rather eye-opening 70% longer. Some of their yeast cells appear to have set the all-time record for the organism, actually. Caloric restriction didn't help extend these, either - the effect was already maxed out, apparently.

What about normal yeast under caloric restriction? It turns out that they have greatly increased PNC1 levels, and the protein was induced under every other condition that is known to increase lifespan. PNC1 may indeed be a key longevity gene, and may be more fundamental to the process than the well-studied SIR2. The researchers run with this hypothesis, suggesting that it explains how so many different methods can lead to lifespan extension - because they're all going through PNC1.

So, how is all this going to play out in higher organisms? It's going to be an interesting line of research, which you can be absolutely sure is being vigorously explored as you read this. One big question is the close and tangled relationship between longevity and cancer. Simple organisms, like C. elegans live their lives with all the cells they're ever going to have. They don't try to keep renewing things, but we and the rest of the complex organisms do. And that means that we have to keep a close watch on the cell cycle.

All the processes needed for cell division have the plastic explosive charge of apoptosis wired up to them, and if anything goes wrong, the ignition sequence is triggered and the cell dies. Or, at least, that's how it's supposed to work. The way most cancer cells start their career is by evading this fall-on-your-sword programming, and their descendants never look back. Attaining longevity through better DNA and protein repair, through minimizing oxidative damage and so on - that's presumably going to be benign. But attaining it through messing with the cell cycle could be a tricky business.

The human homolog of SIR2 is a gene called SIRT1. It's known to be a deactylase as well, and as the authors of the current paper point out, it's also inhibited by nicotinamide. Moreover, the poly-ADP-ribose polymerase enzymes, which are involved in a lot of very heavy-duty jobs like DNA repair, telomere maintainance, and unwinding DNA for transcription of stress proteins, are also inhibited by nicotinamide. "These findings," the paper says, "raise the possibility that nicrotinamide regulates critical cellular processes in higher organisms."

And, it seems to go without saying, raise the possibility that increased nicotinamide clearance might well extend human lifespan. The authors point out that there's already an enzyme, NMMT, which is known to clear nicotinamide by methyating it. Decreased NMMT expression has been shown to increase sensitivity to radioactivity - which makes sense, if some of those DNA-repair enzymes are being inhibited by too much nicotinamide lingering around. But increasedNMMT activity has also been reported: as something that leads to an increase in tumors.

So, the question is still open: can we touch lifespan without triggering cancer? It could be that we've asked Death enough times about where his sting is, and he's finally decided to show us. But that story isn't written yet. Fortunately.


posted at 10:18 pm

Thursday, May 22, 2003

More Bold-Face Stuff

This seems to be Pharma Week over at the New York Times, so that makes it New York Times week over here in the Pipeline. Man, I hope that we're not in for some Howell Raines-style "flood the zone" reporting here, but I'm starting to wonder. Today's story, from the front page, no less, has particular resonance since I just wrote about the tide of lawsuits against the industry, subject of a long article in last Sunday's Times. (You remember, the same day as they dropped that Acme-brand anvil on Bristol-Meyers Squibb in the Business section.)

Unfortunately, this story is one of the ones that shows why the tort lawyers keep digging. It's some 20-year-old stuff from Bayer involving the sale of un-HIV-treated plasma products back when that process was first realized to be necessary. It's not a happy reading experience, for Bayer or anyone else. (It's not just them - as the article mentions, the other companies in the market back then may well have done the exact same thing; there's just less documentation.)

But that's the thing. These days, it doesn't take any 20 years for potentially dirty laundry to get hauled out. Nope, things have sped up nicely these days. And there's a lot more documentation than there used to be, too, thanks to e-mail and all those PowerPoint presentations scattered across the servers. If there are things like this going on now, we won't have to wait until 2023.

Bayer maintains that it did nothing wrong during the period described. But that doesn't mean that good tort lawyers haven't be able to make something out of the material in this article. (everything in it is from lawsuits over the years. This "old-news" angle is probably why Bayer's stock shrugged off the whole thing in trading today.)

But back to the present: given the number of sharks in the water these days, it seems obvious that we don't need to be throwing any more chum out there for them. It goes without saying that immoral and illegal activities shouldn't be taking place, and it should go without saying that companies shouldn't even do things that could be painted that way in court - no matter what side of the line they might really be on. Our industry is being sued enough already. Aren't we?


posted at 9:37 pm

The Hype May Be Real

For some time, tech-bloggers like me, Charles Murtaugh, Richard Gayle, Jason Skie, and the folks at ScienceBlog have been going on about RNA interference as the current Big Happening Thing in biology. (I fully expect the Nobels to start raining down very soon.)

Now Fortune magazine has a cover banner on "Biotech's Billion-Dollar Breakthrough," and it's all about RNAi. It's a nice, albeit compressed, overview of the field and some of companies that are working in it now. If my Nobel guess is accurate (and there's no reason why it shouldn't be; this is big stuff) then the people mentioned in this article will be recipients.

Problem is, there are more than three candidates. In the past, that restriction has led to some delay and confusion in the awarding of Nobels. I think it might be worthwhile to split this one up somehow, either by dividing it into separate discoveries (which could be awarded in different years) or even by shoehorning some of it into the chemistry award. PCR was a Chemistry prize, after all.


posted at 4:33 am

Wednesday, May 21, 2003

Sunscreen Chemistry

I had occasion the other day to read a paper whose chemistry was close to some work I did in my post-doctoral days. I did free radical reactions and photochemistry then, which was interesting, but I've rarely done much of either since.

Photochemistry, especially, has a reputation as a voodoo branch of organic chemistry. There are a lot of odd reactions that can be brought on with the right irradiation, things that you can't get to happen any other way. The standard complaint is that these things are too finicky. The reactions are high-strung and tend to jump the traces a lot - plenty of people who mess around casually with photoreactions end up deciding that it just takes too much optimization.

The other problem, from my latter-day pharmaceutical point of view, is that scaling these things up is a nightmare. I can imagine what would happen if I took a synthesis over to our large-scale labs that had a photoreaction as an irreplaceable step. The response would feature a range of pithy vocabulary-building words in several languages, let me tell you, and I'd be lucky not to leave with my mercury-vapor lamp wrapped around my head.

But there's something appealing about getting new compounds to form just by shining light on things. (One of the fellows down the hall was starting off a bromination that way the other day, which is an ancient reaction that used to be done - before my time! - by putting the flask in a sunny window.) There are reactions that everyone wants (electrolysis of water, plant photosynthesis) that just need light and the right catalyst. There's always someone chasing them.


posted at 8:34 pm

Tuesday, May 20, 2003

Congratulations

. . .to Genentech, on their successful trial of Avastin in colorectal cancer. This news was all the more suprising, and welcome, because the same anti-VEGF antibody had failed pretty thoroughly in a breast cancer trial. (In fact, one analyst came out just before these results were announced, saying that he was downgrading Genentech's stock because of the drug's dim prospects. Oops.)

But all this is a glimpse of the future of cancer therapy. We're only beginning to get a handle on the latest therapies. Right now, we have some drugs that are capable of acting almost miraculously well (Gleevec, e.g.) Even the maligned Iressa, from AstraZeneca, does a tremendous job - sometimes, for some patients. And that's how it's going to be. Cancer is a highly individual disease, and we're now going after mechanisms that are specific enough to be affected by this trait. Increasingly, things are going to work great, or not at all.

That's led, as you'd imagine, to a huge amount of effort to figure out which patients will be in which category. Working that out before you start enrolling people in your Phase II trials would be optimal! And a clear marker would be a tremendous boon to clinical practice - give it to the people it'll benefit, and don't waste the time (and hopes, and money) of those it won't.

The Wall Street Journal's "Ahead of the Tape" column today correctly cited the rule of thumb - to sell biotech companies when the good news of their trial hits. But then the column turns right around and says that this time may be an exception:

Avastin might manage $1 billion in sales at peak, analysts rushed to estimate. Most cancer drugs don't reach that lofty sales target, but once approved, doctors will likely add it into the cocktail with other regimes for other cancers. It's bold, but not outlandish to think of peak sales approaching $2 billion. . ."

Whoa there, Tape-meister! That's actually a reasonable argument, but it may well not happen that way. If we do figure out which patients with which cancers will respond to the drug, then the market for it will immediately contract - because we will, perforce, know which patients won't respond. As this age of personalized medicine (that we all keep hearing about) actually dawns, it's going to cut into the market value of each drug it affects. This isn't a thought you hear expressed very much, but I can assure you that it crosses people's minds.

And there's a potential for cross purposes. As mentioned above, it would be a huge benefit to a clinical development team to know how to target the drug trials for maximum effect. But every time that happens, the marketing people will watch their high-end projections disappear. It's something they're going to have to get used to.

Because overall, the change will definitely be for the better. There's no way to stop it, nor would anyone really want to. But it means, in the long run, that we're going to need more drugs. Each therapeutic area could end up supporting more individual treatments than it does at present, but each of those drugs will have a smaller (albeit very enthusiastic) share. Targeted trials will make them cheaper to develop, but the question is, by how much compared to the smaller market size. It'll be a new world, and it'll be here before we're ready for it.


posted at 9:25 pm

Monday, May 19, 2003

Because That's Where the Money Is

Two in a row! I'm going to break my New York Times link policy again to discuss Sunday's front-page article "Trial Lawyers Now Take Aim at Drug Makers." There are several angles to this story, and the Times doesn't quite get to them all.

Actually, one thing about the story is how it's not exactly breaking news (although it did get fronted above the fold, as the newspaper folks say.) The table that accompanies the article shows the thousands of lawsuits that have piled up around various drugs and companies, and I can tell you that they didn't get filed last week. Most of the drugs in the table were withdrawn or severely restricted up to six years ago. Only two of the six listed are still on the market at all. The list of companies involved is a bit of an artifact, too: Rezulin (troglitazone), for example, is listed as Pfizer's problem - but it was Warner-Lambert's problem for years; Pfizer just inherited it when they took them over.

That said, what about the substance of the piece? We'll get the reflexive reaction of the way first, because you can imagine just how happy I am about all this. This is a really disgusting prospect for the industry. Everyone who works at a large drug company (like I do) has shivered at the first winds of a possible lawsuit storm. All you have to do is look at the asbestos situation; there's the possible future. First all the large companies got stripped of assets, then the lawyers moved on to the secondary money pools. Every company that even touched anything that had asbestos in it has been sued by now. It's an industry, a wonderfully profitable industry.

So now the tort lawyers want some of the pharmaceutical sector, do they? The approach is the same as in the asbestos cases, as the Times correctly points out. First, the lawyers search for plaintiffs. Radio ads, newspaper ads, internet solicitations - why chase ambulances if you can rent a flashing sign on the side of every one of them in town? But there's a pecking order to the cases that turn up: If you're ready to sue, but you're in, say, Delaware, you can just take a number and have a seat. Because there are cases in Texas to be tried first, cases in Mississippi and West Virginia. You know, the states that traditionally give huge jury awards. Where else would you kick off the party? If all goes according to plan, one or more of these will strike a money gusher.

Then the screws get applied: "You can go on like this," the companies are told. "We've got plenty more cases lined up. And did we mention that we're seeking class action status? Or you can pony up some serious money right now - at least you'll know what the bill is. If these suits just keep coming - we can't stop these folks! - who knows what it could add up to?" As the Times article says, companies run this risk if they contest the first cases and lose. If they try to dodge things by paying people off in big out-of-court settlements, though, that can set off a feeding frenzy of its own. From a company's point of view, perhaps the best strategy is to fight an early case or two with everything you have, while settling as many small cases for as little money as possible.

How valid are these lawsuits, anyway? The article does a reasonably good job here. It's correctly pointed out that all drugs have side effects, which is a lesson that has been repeated so often that many people have just tuned it out. And Janet Woodcock of the FDA makes a good point, that more people are taking medication than ever. (I'd like to see what the increase in people who are taking more than one chronic drug prescription might be; I'm sure it's huge. Many of these people are older, as well, and more susceptible to problems of every kind.)

But the lawyers disagree, of course:

Plaintiff's lawyers say that their new aggressiveness has not led them to attack good drugs. There's a circular definition for you - DL.) Instead, their new resources and methods have simply made them better able to press claims in what they say are the many cases when companies introduce dangerous drugs and hide their risks - which they say the FDA does not adequately monitor once drugs are approved.

Well, speaking as an insider in the halls of said industry, I can tell you that we're afraid enough of being sued already, thanks. Any company that doesn't think about such risks isn't long for the world. At every stage of clinical development, the thought goes through your head: Is this going to sink us? Is there a side effect here, a dosing error that could be made, that could open us up to liability? There is always something, as Willie Stark said in All the King's Men. Every drug, from aspirin on down, can be trouble. An epidemilogist at Harvard is quoted as saying that "this is something we have to live with." He's right. But why live with anything when you can sue?

It's worth comparing a couple of other major complaints about the drug business, to see how they fit in with the lawyercentric view. Is this the same industry that's been accused of cranking out imitations of itself, profitable me-too drugs that don't add anything to clinical practice? When did we find the time to unleash all these dangerous new medicines, then? And is this the same FDA that's been hammered for delaying a whole list of life-saving wonder drugs because of bureaucratic foot-dragging, always bleating for more clinical data?

Just checking. Because, as far as I can tell, the pharmaceutical industry, for all its flaws, is a unique resource. The benefits of sticking it really good and hard escape me.

Update: Support inside the legal profession - at least, the part of it outside the mansions of Tortville - from Ernie the Attorney. And DB over at Medical Rants finds himself checking his pulse as this topic makes him defend the drug industry. Medpundit adds "God save us from the lawyers."


posted at 8:08 pm

Sunday, May 18, 2003

Ouch

While I'm mentioning the mail, I wanted to say that my industry readers are a minority, but a vocal one. I don't get that much traffic from Bristol-Meyers Squibb, but everyone else seems to be on board. Pity about that exception, because I was going to extend my condolences to them for the really brutal article about their CEO that appeared in the New York Times today. I don't usually link to the Times (because of their free-for-a-little-while policy,) but I'll make an exception for this one. It must have really caused some dropped forks and spilled coffee in central New Jersey. . .


posted at 9:39 pm

A Chord Is Struck

Last week's piece ("Pyrex Flasks Don't Bite Your Finger, Either") has generated some interesting mail from my drug-company readership. For example, a friend from one of the larger outfits writes that one of his collegues n the in vivo biology group recently got dragged over the coals because the latest round of rodent data was a bit off in the control group.

That's a cheap shot, of course. And it's good to mark down the people who go crazy about that kind of stuff, to put them on a list. They either don't have a good understanding of what they're seeing (in which case they should consider keeping quiet until they've done some homework,) or they understand perfectly well that animal data vary. But they just want to show that they're on top of things, that they're real hard chargers who don't let anything get by them. There's a word for such people; let's all mutter it together on the count of three. . .

Another reader, from yet another whopper company, writes:

On days when I actually have a minute or two to daydream, I imagine a wonderful world which mirrors our own with only one glaring difference: med chemists are taught at some point during college that biology is so complex, a two-fold difference ISN'T SIGNIFICANT. I knew exactly when I went from wide-eyed neophyte biologist to grizzled, hoary veteran. It was when I spent 15 (fruitless) minutes trying to explain this very point to a young man who has since switched into the "business" side of science (presumably because accounting offers very few examples of error bars).

I've seen that one, too. As I mentioned, it's hard for someone new to the science to get used to how fuzzy the numbers start getting. To put it in terms of one of my leisure time activities, amateur astronomy, people are also surprised when they see how the view through even a large amateur telescope doesn't match the Hubble or ESO pictures they're used to seeing in the magazines. Someone with more experience just rides it out, sets up their scope in a favorable location, in the right kind of weather, and waits patiently for the clear moments. You want angular resolution, you make the baseline of your mirror larger. You want to see clear in vivo effects, you make the number of subjects larger. Things will gradually come into view.


posted at 9:34 pm

Thursday, May 15, 2003

More Ariad

Since I mentioned Ariad's lawsuit against Lilly yesterday, I should note that there's been some news on that front recently. This week, a judge rejected a motion by Lilly to have the suit thrown out. It'll grind ahead, as scheduled.

Ariad's shareholders reacted pretty heartily to the news (check this chart of the week's trading.) But that trading would seem to me to be either misplaced optimism (we're on! we're going to win!) or surprised pessimism (hey, whaddya know, the judge actually let us keep going.) Either way, I don't see it as a strong Ariad vote.

It's just too early to tell. That's why this isn't such big news, because the only way the suit would have gotten tossed out would be if it were clearly baseless. And it's not - Ariad has an issued patent. That alone means, almost every time, that things are going to end up in court or in a settlement of some sort. Once your patent is issued, you do have some real leverage.

But not all issued patents hold up - or, at least, not all their claims do. And not everyone interprets the meaning of the remaining claims the same way. It's going to be a while until we see what happens. Any trial would start next year sometime, and that's assuming it moves right along. (Lilly will doubtless be spinning things out as much as they can.)

I'd advise both Ariad and Lilly shareholders to base their decisions on something else for a while.A telephone psychic will give you as much insight into the merits of the case as all this pre-trial maneuvering can.

Meanwhile, Ariad is still in there pitching. Their CEO, Harvey Berger, is quoted in the above item as saying "Our objective now is to proceed expeditiously to trial and to seek a damage award based on a reasonable royalty on Lilly's sales of Evista and Xigris, as we continue to pursue additional licenses of our NF-(kappa)B patent portfolio." Portfolio is a rather rich word for a single patent, don't you think?

And as far as "pursuing additional licenses," that seems to mean sending out more ominous letters, one to every company with a drug that looks like it might brush up against NF-kappaB. They seem to be keeping their eyes on company pipelines, alert for anyone they've missed. What a way to make a living.


posted at 9:04 pm

Wednesday, May 14, 2003

Velcade Makes It Through

The big news this week has been the FDA approval of Millennium's Velcade for multiple myeloma. This comes only five months after they went to the agency (two months after the application was accepted) which is extraordinarily (and enviably) fast. The New York Times ran a long piece this morning (which I won't link to, since after a few weeks they'll ask you for money to see it.) At any rate, Matthew Herper at Forbes had much of this story six months ago.

As many have noted, the FDA seems, under its new leadership, to be pushing things out the door more quickly. The recent approval of AstraZeneca's Iressa is another case in point. It doesn't seem be be effective in most patients, there are questions about its side effects in Japan, and it completely failed to show any effect as a combination therapy. But the FDA decided to grant its approval, in the remaining window of treating patients who have already failed conventional measures. It'll be interesting to see the extent of off-label use. . .

Velcade's a similar story, although the FDA advisory panel was more enthusiastic about it. It's been approved for patients that have failed at least two other treatments (which is about a quarter of the patient population; multiple myeloma is a very nasty condition.) That's still only between ten and twenty thousand patients, though - this isn't going to turn MLNM into the next Amgen. But it's a solid advance, and it was done under difficult circumstances. The Forbes and NY Times articles have the details. This compound is a story in persistance, through mergers, funding problems, and various raised eyebrows over its mechanism (and the fact that it has a boron in its structure. No one's every taken an organoboron compound all the way before.)

It's billed as a proteosome inhibitor, which is certainly true. That's yet another wrecking yard of the cell. Plenty of proteins important for cell growth are dismantled there, and the original idea was that disrupting this process could throw off the whole cell cycle. That's a pretty scary mechanism, but tumor cells were thought to be more vulnerable than normal ones (which is an idea with a long history in chemotherapy.) In addition, Velcade's activity is quite reversible, which should give you a little more margin of safety than something that binds more strongly.

Of course, Millennium has a reputation as a genomics-driven company, and this doesn't quite fit that story. The Times article has a quote from Raymond Deshaies of Cal Tech, who's characterized as "finding it odd that Millennium's greatest success to date is a conventional drug." "What's the thing that's going to make them?" he's quoted as saying. "A sledgehammer, rat poison. It's the opposite of personalized medicine."

Well, I'm not so picky, I guess. Millennium would also like to have a reputation as a profitable company, and they'll take what they can get. The genomics stuff is not going to pay off for a long time: let's count the number of genomics-based drugs they have in the clinic. Right. Companies do all kinds of things to make money to keep the research going, because no money, no research. It's the same as in politics - you can't do anything until you get elected, so you pull out the stops to accomplish that much. If MLMN has to cure a few people of multiple myeloma along the way, well, all I can say is that I'm glad that they swallowed their pride.

But there's one more wrinkle to the story. Velcade also blocks the actions of a protein called NF-kappaB, and that means, I should think, that Millennium is going to be hearing more from Ariad's lawyers. I wrote about this situation several times on my Lagniappe site, but here's a synopsis: Ariad, a small biotech company, is the assignee of a recently granted patent (from a group of heavy hitters in cell biology) which covers just about everything you can imagine around the NF-kappaB protein. NF-kB turns out to be very important player in cancer, inflammation, immune disorders and more besides, and Ariad has adopted a policy of threatening to sue anyone whose compounds work through an NF-kB mechanism. Unless, of course, they pay up. That works for them. In the case of Eli Lilly, they'd already gone through the threat stage - Ariad press-released their lawsuit against LLY five minutes before they sent out the release about their patent, which gives you a sense of their priorities.

So, now that there's money to be made, I'm sure Ariad will be homing right in on it. A couple of my correspondents know more about this situation than I do; we'll see if there are any developments.


posted at 9:13 pm

Tuesday, May 13, 2003

Pyrex Flasks Don't Bite Your Finger, Either

All this talk about cell-assay problems should remind people of Heisenberg's Uncertainty Principle. Unlike physics, there's no mathematical law involved here (that anyone's aware of, that is) and thus the uncertainly isn't quantifiable. (Yep, the one thing that isn't uncertain about Heisenberg's principle is the degree of uncertainty involved - that you can work out very well indeed.)

But the principle of the observer perturbing the observation is very much with you while you study any living system. It's a problem that the nanotech people are going to have address, as I mentioned last week. Being poked with carbon nanotubes or peppered with small metallic particles are very odd experiences for a cell, and they're surely going to have some effects. Will they be enough to raise suspicions about the data?

And as yesterday's post outlined, just taking a cell out of its normal environment is almost always a guarantee of making it behave unnaturally. That's why we can't use cultured hepatocytes to check out the stability of our drug candidates against liver metabolism: cultured hepatocytes aren't liver cells any more, not in the ways that matter to us. Any time we use cultured cells, we have to convince ourselves that the processes we're studying are close enough to the real situation to make them useful. Trying to bypass that reality checkpoint can lead to serious trouble.

The problem just gets trickier as you go up from cells. You can take pieces of organ tissue and get them to act realistically - well, sometimes, and for a little while. There are, for example, liver slice assays to test compound stability, and ring-shaped slices of intestine have been used to assay absorption of drug candidates from the gut. But such things depend on the cells involved not getting word of their new situation, and you have to be careful not to push things. Variability is a major problem, too. It's a concern with cells, but it really starts to bite down with tissue assays.

Speaking of variability, the next step is assays in whole animals. Drug companies go through a whopping number of mice and rats every year; this should come as no surprise to anyone. But the reason isn't that we test all our compounds in animals - I can't even imagine how many animals that would add up to. (Large companies generate new compounds in the ten to the 4th/5th range per year.) No, we use a lot of rodents because each assay has to be dosed in multiple animals just so we can begin to trust the numbers.

New medicinal chemists are always taken aback when they see the variability of an in vivo assay. It seems hard to believe that the same compound could show such a range of responses. You can see the new hires thinking "Now, if my chemistry worked that unreliably. . .I'd be fired! Why haven't these biologists been fired, eh?" But it's not the fault of the animal pharmacologists (at least, it had better not be!) If you're going to fire someone, you'd want to fire the rodents, and who would replace them?

Out of eight mice, two of them may nearly ignore your drug, as if you'd given them corn syrup. Two others might react wildly, vigorously, almost too strongly. And the other four will scatter in between. Three animals per data point is really the minimum, and often that's worthlessly low. You'll have two lining up together, and one off at the other end of the range, making your error bars an ugly sight. No, a well-controlled rodent study with enough statistical power to convince anyone begins to run to a lot of rodents - a few dozen is about right.

You'd better treat 'em right, too. Mice and rats are creatures of habit. They want their dark and light cycles to run just the way they want them - one janitor throwing on a light switch in an animal facility can blow everyone's data. The food had better taste the same, too. No new suppliers, nothing stale or odd-smelling. And no sudden loud noises, because stress hormones can kick your numbers all over the place. Being a lab rat is stressful enough, and you add to the strain at your peril.

So if you want to see the observer altering the observation, just come down to the mouse rooms. You can alter the data yourself, by slamming the door or wearing loud cologne. There's no way around it. We just have to live with it, and live with what it does to our data. All the alternatives are even worse.


posted at 10:52 pm

Monday, May 12, 2003

Jackpot?

Sometimes pharma companies remind me of the guy in the old poker story: the fellow who had lost three cars over the years, betting big while drawing to inside straights. He lost the first two when he didn't fill his straight - and the lost the third one when he did.

As far as I can tell, most companies have set very aggressive goals for drug discovery. No one's all that happy with their pipeline (well, maybe Eli Lilly is, as today's Wall St. Journal pointed out, but they don't have much company.) So, understandably, many companies are trying to grow out of the current hole by coming up with some winners, fast.

But what will people do if some of these actually pan out? If you send a bolus of projects into the development side of the organization, odds are that they won't be able to handle them all at once (especially if they haven't had much to do lately!) They'll have to sort them out by possible market value and time sensitivity (patent life, competition, etc.) That means that some projects will head on toward the clinic, and others will, of necessity, sit on the shelf. Where, it's safe to assume, they won't be doing anyone much good.

Depending on the therapeutic area, projects can take up a lot of room in the clinic. At my previous company, we had a schizophrenia therapy that showed poor performance in Phase II trials. There was a chance that a longer, larger trial run in a different manner might have demonstrated efficacy, but the organization decided that the money could be better spent somewhere else. By that time, my lab and others had moved on to Alzheimer's - and our comment was that if they didn't like the expense of a dementia trial, then Development had better hope that we never came up with anything for Alzheimer's. (And for several years, we obliged them, but that's another story.)

I'd say that sending a project off to the shelf is a waste of time, unless someone has some very good reasons up front why it wouldn't be (and those would be interesting to hear.) But everyone who's worked at a large company has seen projects delivered out of the research organization that were DOA in development. So, just who is it that benefits from such exercises?


posted at 9:48 pm

Sunday, May 11, 2003

Cells With Short Memories

I mentioned in last week's roundup of nanotechnology that the single-cell analysis ideas might suffer from a common problem - that single cells don't behave the same way that they do in the intact organism. There's a good example of this in a new paper (Horm. Metab. Res., 2003, p. 158).

A group at INSERM (Toulouse) has been looking at human adipose cells, which are widely studied. Fat tissue is obviously important in the discovery of drugs for obesity and diabetes, and it's a big player in osteoporosis research as well (both adipose tissue and some varieties of bone tissue are derived from the same precursor cells; they just get different developmental signals.) Adipose tissue has also, in recent years, been recognized as an endocrine organ. There are plenty of metabolically important signaling peptides produced by adipocytes, and they're a key target for several others.

Human adipocytes aren't the easiest cells in the world to get (no human tissue is the easiest) but they're a lot more available than some of the other human types. (I was on a project once that needed a particular human tissue type to answer a key question, and we were on the waiting list at the local hospitals. But nothing ever came up, for various reasons, and the project just sat there. It got to the point that one of the biologists took to noting unhelmeted motorcycle riders on the highway as he came to work in the morning, speculating on their likelihood of having filled out organ donor cards. . .)

The reason you can get human adipocytes is easy to explain: liposuction. (Visions of Matt Groening's "Akbar and Jeff's Liposuction Hut" come immediately to mind: "Where the Elite Meet After They Eat, So They Can Once Again Be Petite!") You can get these cells directly from the source, or buy them from vendors after they take them through various sorts of cell-sorting and purification. But how good are they?

That's what the French team has investigated. They took the primary cells and kept them going under cell culture conditions, just what you'd need to do in the lab. Over a two-day period, they monitored their response to typical stimuli, and they also ran them through some gene-chip assays (looking for changes in messenger RNA for a panel of proteins that are specific to adipocytes.) They found "a rapid and dramatic decrease" in the mRNA for a number of the important ones, as it turns out, and their list includes a lot of the things that you'd use to define a working adipocyte. Meanwhile, several other things starting coming up, and some of them (like tumor-necrosis-factor alpha) would be expected to have some profound effects, too.

They did find some tricks to keep some of this from happening, but it illustrates the trickiness of dealing with highly specific cell types. These guys live among their kind, and they live in constant communication with many other cells. Take that away, and all bets are off. Reductionism is a great way to find things out, but it can only take you so far.


posted at 5:53 pm

Thursday, May 8, 2003

Address Unknown

As for all this nanotech, you can see that a constant theme is getting things where they're supposed to go - thus the emphasis on coating things with antibodies, recognition proteins, DNA oligomers, and so on. That's a major task that the cellular machinery does tremendously well, and at which we medicinal chemists are complete bozos.

We have enough trouble just getting our compounds out of the intestines and into the blood; subtleties past that are often out of our range. As far as targeting things to specific spots inside the cell, that's generally not even attempted. What we shoot for is selectivity against the enzyme or receptor we're targeting (as much as we can assay for it, which sometimes isn't much.) Then we just try to get the compound into the cells and hope for the best.

It's assumed that we're basically soaking the cytoplasm with the compound, but there really haven't been many studies done to look at intracellular movement and disposition of pharmaceuticals. That's mainly because those studies are quite difficult - the best way to do such a thing is with a fluorescent molecule (or one with a fluorescent tag,) and it's often impossible to get a good tag and keep your base molecule's activity. There are several ingenious techniques that are being developed in the proteomics field, though, and these might help us out (more on that at a later date.)

Many of the impressive things that cells accomplish are done through very precise targeting and compartmentaliztion. Almost all cells, for example, carry around enough protease enzymes to complete destroy themselves - if they weren't tucked away in pockets like lysosomes, that is. There are so many cellular processes that use common intermediates (as signals or substrates) that traffic control has to be exquisite for anything to work at all.

Cyclic adenosine monophosphate ("cyclic-A" to its many admirers) is a good example. I can't begin to count the number of important pathways that use cyclic A - dozens, hundreds, more? And most of these are going on at the same time. The stuff is being generated, recognized, and degraded in very tight and specific patterns. Coming in med-chem style and flooding the cell with a close mimic of cyclic A would be an addled idea indeed. You'd be hitting the brakes, the gas, the horn, all the turn signals and trying to play six different songs on the radio simultaneously. And into the nearest tree you'd go. We can play the cyclic-A game, up to a point, but not that way.


posted at 9:22 pm

Wednesday, May 7, 2003

On the Cell's Own Turf

The May 1 issue of Nature has a neat article (p. 10) on the interface between nanotechnology and molecular biology. Given the emphasiss on small structures in my first two posts of the week (below,) I thought this would be a good time to highlight some of this work. It's a weird and interesting lineup of ideas, some of which are clearly a lot closer to producing useful devices than others. Some of these things are going to turn out to be wastes of time, but not all of them are. And the ones that aren't could do things that no one's ever been able to do.

One gizmo (the nanolab) from a collaboration called the Nano-Systems Biology Alliance lets cells sit in small silicon containers, with a pore in one side to allow access to the cell membrane. The chip side has hundreds of nanowires, which can be coated with reagents. For example, you could layer them with specific antibodies to detect secreted proteins, or with DNA fragments to detect complementary messenger RNAs. As a reality check, the DNA oligomer technology is the basis for the popular - albeit often uninterpretable - gene chip assays, and the extension of this technique to nanowires has been demonstrated in individual cases. The Alliance has a new technique for fabricating nanowire arrays.

These folks envision having about a thousand cells per chip, each in its own box, and each one being queried by its own different probe (each of which could have hundreds of different nanowires.) Potentially, you could get real-time readings on what proteins are being secreted (through your antibody nanowires.) As the article points out, there are some problems. The fluid that the cells are living in tends to disrupt the connection between the cell membrane and the probe, unless a low ionic strength medium is used, but that's an unnatural stress on the cells. (I'd think that sitting in a silicon chamber would also be an unnatural stress, frankly. There are plenty of cell types that only grow to their proper function when they're surrounded by their fellows. "Confluency," the state of having a smooth layer of cells with their membranes touching each other, is a standard cell culture state that's often desirable, and unattainable on the nanolab chip as described.)

Another nanotechnology with some interesting applications is the "quantum dots" idea. These are similar to the drug-delivery micelles that I spoke of earlier in the week. You could also use them to deliver a reagent (which fluoresces, for example) to specific targets in the cell. As in the drug delivery application, it would all depend on what you coated the thing with. (Unfortunately, in each case, there are many intracellular things we'd like to target that we don't know how to specifically interact with. That's a situation that's improving with time, though.)

A truly weird extension of this idea has been tried at MIT. Gold nanoparticles were attached to large biomolecules (either a DNA sequence or a protein.) Then the particles were subjected to an RF field, which made them heat up. The localized heat caused the molecules to denature and adopt new conformations, but not permanently. Things seem to have gone back to normal when the field was removed. If these particles can be targeted specifically enough, you could potentially have an electromagnetic monkeywrench to toss into specific cellular machinery.

That brings up a point that the Nature article addresses, to its credit. With all these odd modifications, how do you know that you can trust your data? Will the experiments with gold nanoparticles, for example, only tell you about what happens in cells that have been unlucky enough to ingest gold nanoparticles (and are feeling the strain?) Any new idea in this field is going to have to undergo a lengthy shakedown. Although things are developing quickly, these techniques are not going to come on line as quickly as some people think, just because of this validation problem.

But I think the general trend is unstoppable. If we're going to understand the cell, we're going to have to get inside it and mess with it on its level. There are doubtless plenty of great ideas out there that haven't been hatched yet (or have been and are being kept quiet until they've been checked out.) For example, I'd be surprised if someone isn't trying to mate nanotechnology with RNA interference in some way. (There's a hybrid of two hot fields; I'll bet that grant application gets funded!) It all bears watching - or participating in, if you're up for it.


posted at 10:07 pm

More on the Scientific Comments Proposal

For some interesting takes on the public-comment idea below, see this post at Hublog and by John Vu. The scheme seems to have struck a chord with people - I know when I read the Nature letter, I though "Sure. . .why don't we have that already?"


posted at 10:02 pm

Online Science

There's a neat letter in the latest issue of Nature (PDF here). David Eagleman of the Salk Institute and Alex Holcombe of UCSD are proposing something for the scientific literature that every blog reader is familiar with: an online comments section. (Their examples aren't blogs, though, but rather things like Amazon's book reviews.) The comments would be accessible from the paper's record in the PubMed database.

They've seemingly followed the experiences of other such systems, because they immediately propose at least some mild form of moderation ex post facto, giving someone the ability to remove "unhelpful or libellous" comments. They're also suggesting a password be used, and that every comment be associated with a working e-mail address, with no anonymous postings permitted. They've also noted what happened across Usenet during the 1990s: "Automatic advertising posting can be prevented by a requirement to key in a text code readable only by humans."

I'm sure that some people will find a way to abuse this, no matter what safeguards are added. Nobody reading this has to be told what some people are like when they get a chance to vent online. But I think this is a really good idea, and I hope it catches on. A few journals have already experimented with the idea on their own (although, as far as I can tell, none of them in my particular field.)

The idea is that people could debate the points of a paper, make suggestions for further research, ask questions, and mention if they've been able to reproduce any of the results. Eagleman and Holcombe point out that minor (and major) criticisms of published papers rarely catch up with the work itself, at least not in any form that anyone can find. Even formal retractions have a hard time; people cite retracted papers without even realizing it.

I can see how this could work out in chemistry, for example, because the barriers to replication are often smaller than they are in the biological sciences. There will be people who will be afraid to post their best criticisms, for fear of tipping their hand about their own publication-ready research (but that means that their ideas are going to make it into the literature, anyway.) And the psychological pressures of critiquing a paper by some big name will make themselves felt, too. But, overall, I think this could be a real advance. It'll be quite interesting to see what the signal-to-noise will be if this is implemented, though.

The authors are actively welcoming comments on this proposal, as well they should, given its nature. Instead of e-mailing me about it, send your thoughts to eagleman@salk.edu. (Of course, you can always mention where you heard about it!)


posted at 7:26 am

Monday, May 5, 2003

Sneaking Into the Cell

The same issue of Science that I spoke of yesterday has another very interesting article, this one on drug delivery via micelles (p. 615.) It's put in context in an excellent brief review of the field (p. 595) by Jeffrey Hubbell in Switzerland. I won't attempt to summarize the whole area here; read both articles for the real details. But it's certainly worth a look, especially considering the topic of yesterday's post.

That, of course, was about the trouble caused by small spheres of amyloid proteins. Those things are around 3 or 4 nanometers wide, which put them right in the range of things that cells are used to dealing with. There are plenty of proteins that are much larger than that, and plenty that are smaller. (The drugs that my colleagues and I make belong to an even smaller order.) There have been many attempts over the years to use small hollow constructions on slightly larger scales (generally 20 to 100 nm) to deliver drugs, and it looks like some of these are starting to actually work.

Which is good news, because we medicinal chemists can use all the help we can get. Our compounds, despite our best efforts, seem to be getting bigger and greasier all the time (more on this at a later date.) And that means that they're having more trouble getting out of the gut - and once past that barrier, more trouble making it through the liver without being chain-sawed apart by gleeful metabolizing enzymes. Hiding our drugs inside some innocuous-seeming shell could be just the ticket.

There are plenty of approaches being tried. Polymers are being generated that contain regions that are attracted to cell surfaces, for example. Once there, they get taken inside in small internalized bubbles (endocytosis.) That's not a complete solution, though, because these pockets (endosomes) are actually designed by the cell to be a dead end. Their interiors are gradually made more acidic, through proton pumping, and they're eventually merged with lysosomes, which is like tossing them into a garbage disposal.

These latest micelles escape being chewed up by the vicious lysosomal enzymes, though, giving the associated compound a chance to bail out. The research team was able to see intact micelles adrift out in the cytoplasm of the cell, which suggested that they affected the endosomal membrane enough to be able to slip out through it entirely. Taking a more active approach, other groups have incorporated proteins that are specifically designed to cause endosomal disruption.

A particularly tricky method is to appropriate some proteins that HIV uses. These cross the membrane intact, with no endocytosis involved, through mechanisms that still aren't all that clear. But hitching a drug to such sequences could be a way to just fade it across the cell membrane, and this could work for structures that otherwise wouldn't have a chance.

Some of these same ideas are being used to deliver DNA and RNA into cells, which is not always an easy process (taking up unknown nucleic acid sequences from outside is not something cells have evolved to do cheerfully.) Such techniques are probably going to be key to getting RNA interference techniques to work therapeutically; the current methods tried in animals have really required brute force that could never be translated into the clinic.

There's been a lot of interesting work published in the last few years. The field seems to be making real progress, this after a good 20 years of speculation and semi-successful attempts that were hard to generalize. If anyone comes up with a broadly applicable way to deliver small molecules, they're going to do very well for themselves indeed.


posted at 10:17 pm

Sunday, May 4, 2003

Amyloid Diseases - A Breakthrough?

There's an interesting and potentially very important paper in the April 18th issue of Science (p. 486.) If it pans out, this could lead to simultaneous breakthroughs against a list of terrible diseases. At the very least, it's provided a big step forward in understanding them. This should be getting more press than it is, frankly.

A team from UC-Irvine has been studying amyloid proteins, a class that causes all sorts of trouble. Perhaps the most famous amyloid is one that has long been suspected as the cause of Alzheimer's disease. The brains of Alzheimer's patients always show plaques of precipitated protein, surrounded by dying neurons. The protein always beta-amyloid, 42 amino acids long in most cases, which is cut out of a larger protein called APP (amyloid precursor protein.) Vast amounts of effort have gone into finding out which enzymes do the cutting, where they are, why they do it, and so on. What's for sure is that APP itself is found all over the body, in places where beta-amyloid never shows up, so it's something peculiar to the brain.

(There's another protein abnormality in Alzheimer's - the neurofibrillary tangles. These have a different protein, called tau, and no one's really sure where they fit in. Are they a cause of Alzheimer's, or an effect? Actually, you can get people who ask that about beta-amyloid, too, although the weight of the evidence is toward "cause.")

At any rate, there are other amyloid proteins out there. They're small sequences that precipitate abnormally, clumping up and coming out of solution in body tissue. Prion proteins, implicated in "mad cow" and other encephalopathies, are one, and alpha-synuclein (which does the damage in Parkinson's disease) is another. Over the last few years, it's become clear that these proteins have some things in common, although they're pretty different in their amino acid sequence. For one thing, they seem to bunch up in a similar manner - they start off by forming roughly spherical aggregates, of just a few protein units, and these then start to clump together themselves, often in chains. As this process goes on, fibrils of insoluble protein start to fall out.

A big mystery has been just what causes these things to be so toxic. It's tempting to speculate that the damage happens when the stuff comes out of solution, but evidence has been mounting that it's the small, soluble forms that are the real problem. This latest work dramatically boosts that theory. What the Irvine team has done is generate antibodies against beta-amyloid that react against the first stages of aggregation - the spherical oligomers. They don't recognize the later stages, or the insoluble fibers, and (interestingly) they don't recognize the protein if it hasn't started to oligimerize, either. Just the spherical stage.

When they look at brain tissue from Alzheimer's patients, they see some interesting differences compared to looking at the insoluble amyloid plaques. They're in the same region, but not on top of each other. It's clear that the spherical oligomers are a distinct species, and that they're found in the diseased brain - and it looks very plausible that they're a first stage in the disease. The antibody doesn't recognize the tau-protein tangles, and it doesn't recognize APP.

But wait, as they say, there's more. When they tried their antibody on the other amyloidogenic proteins, they found the same behavior. Nothing with the monomer, nothing with the large insoluble stuff. It just picked up the small spherical forms, and it picked up all of them.

This strongly suggests that all these diseases have a fundamentally similar mechanism. There seems to be something about the structure of these proteinaceous spheres that's toxic, and the structure seems to be similar, in some basic way, in all the amyloid proteins that have been checked. These cause trouble in many different tissues and cell types, so it must be a nonspecific sort of toxicity. In fact, some of these precipitations happen inside cells, while others happen completely outside them, so it must be a very fundamental sort of toxicity indeed. The authors guess that it's something to do with cell membranes, which is a good shot. I'm at a loss to think of anything else that fits so wide-ranging a pattern.

Well, I've mentioned Elan's attempts at a beta-amyloid antibody before. Would a more specific antibody like this one be clinically useful? The Irvine groups tested the idea in cell cultures, and found that their antibody protected cells from all of the toxic amyloid peptides. That's a key first step, and an exciting result. If they're not rushing to try this out in animal models, then they're fools. And this paper argues very, very strongly that they aren't fools. Could this the beginning of an attack against a host of terrible incurable diseases, all at the same time?


posted at 10:50 pm

Thursday, May 1, 2003

See You on Monday

No time to do an update tonight, so we'll roll over to next week. In the works are some items about a new obesity treatment (well, it might be one. . .), a surprising immunological connection between several diseases, and more.

In case anyone's wondering, my reaction worked fine. I had to kick it a bit this morning with some more reagent, but it seems to have finished up well. By the way, for my non-chemist readers, if you ever have to fake a knowledge of chemistry technique, just mention that (of course) no one orders the "tetrakis" palladium catalyst from the Aldrich supply house. (We order plenty of other stuff from them, never fear.) But Aldrich's catalyst has been inconsistent for years; the cognoscenti order theirs from a company called Strem. That should impress 'em. . .


posted at 10:08 pm









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About: Biotech/med
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Organizations

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Scientific Quotations
Dictionary of Scientific Quotations


If the Universe is Teeming with Aliens. . .
If the Universe is Teeming with Aliens
(Then where is everybody?)


The Night is Large
The Night is Large
A Martin Gardner collection


Scientific Anecdotes
Eurekas and Euphorias

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