The State of the State of the Art

This fall will mark my fifteenth year in the drug industry. Looking back at what things were like in late 1989, there's one thing that I find striking above all the others: that very little has changed.

Fifteen years is a pretty long time in the sciences. In a field like molecular biology it's a ridiculous length of time, but their clocks will slow down on them, too: the previous span (from 1974 to 1989) was a much bigger leap for them than the last fifteen years have been. In a mature field like chemistry we don't have such dramatic interludes, but you do see the changes piling up.

But when I started doing drug discovery, it worked like this: you got a chemical lead by random screening, and a bunch of chemists started in on it, changing the structure around to see if they could improve its activity in a set of in vitro assays. The better compounds went into a rodent model of efficacy, and you checked the blood levels of compound to get an idea of its pharmacokinetics. Once you met all the criteria you'd set, you started high-dose toxicology on selected compound in more rodents, then larger animals. And if things held up, you declared a compound to be the winner, and passed it on to the clinical development team (the scale-up chemists had already been having a look at it, to make sure that they could supply enough for longer tox and human trials.)

Sound familiar? That's exactly how we do it now, most of the time. Oh, the compound you started with might have come from a combinatorial chemistry library this time (although odds are that it didn't!) And you might have some help from the molecular modeling folks along the way (but there are plenty of projects where they can't help, and plenty where they only think they can - no offense, guys.) You'll probably have a more assembly-line approach to getting some quick-and-dirty animal dosing for blood levels, too.

But these are minor changes. Are we ever going to do things really differently? Routinely start with an in silico lead compound, say? Build our compounds by mix-and-match fragment assembly instead? Find a way to predict pharmacokinetics, at least a little bit, so we don't have to run everything through mice? Get some serious clues about toxicology, so we can get off the mouse-rat-dog treadmill on the way to human trials?

The cockpit looks pretty much the same as it has for years. All we have are fancier propellers and slightly more responsive rudders. No one has invented the jet engine yet, and I wonder when someone will.

Things I Won't Work With: A Nasty Condensed Gas

If you cool things down enough, you can turn almost anything into a liquid (or into a solid, if you're really insane about it.) Chemists use liquid ammonia fairly often, for example, though it's been some years now since I've needed any. People outside the field think of the aqueous solution of ammonia gas (household ammonia) when you say "liquid ammonia", but I'm talking about the pure stuff. Cool the gas down below about -33 C, and you'll condense it out to a clear liquid that's sort of like a thinner version of water.

It's easy enough to do, with an ammonia tank and a condenser full of dry ice. But once, over twenty years ago, I had a chance to see someone use one of those rigs to condense something a bit more exotic: pure hydrogen cyanide. That's another one that people confuse with the aqueous solution. But pure HCN has a fairly high boiling point, for such a small molecule, and condensing out is no problem - as long as you have more nerve than you have sense.

The fellow doing it was down the hall from me in graduate school, and he was doing an obscure reaction which forms a geminal dinitrile, which themselves are rather obscure compounds. (That's probably because this bug-eyed route is the best way to make 'em.) He was dressed in full suit and respirator gear, for which he'd had to get trained. Everyone else had cleared out of the lab, but someone was watching him at all times from the hallway, just in case.

I thought to myself, "When am I going to get the chance to see pure liquid HCN again?", and went down to see, ready to bail out if anything started going wrong. It looked just like ammonia, clear drops rolling down the cold condenser and dripping into the round-bottom flask below. But there was enough HCN in there to kill off the lot of us, if (im)properly handled.

I've worked with plenty of cyanide since then, and even plenty of reactions that have produced small whiffs of HCN vapor. (As I think I've mentioned, it doesn't smell as much like almonds as it's said to, in my opinion.) But I doubt very much if I've worked with enough of it to match the amount that I saw in that flask, that day - there must have been a couple of moles of it in there. A lifetime supply that was, in many sense of the word. . .

Silent Mutations and Noisy Ones

One of the comments in my post on animal models prompts me to write a bit more on mutations. I stated that the mutant animal models that we use all have something wrong with them, but I didn't mean to imply that all mutations will do that. There are plenty of so-called "silent" mutations out there, single amino-acid changes in large proteins that basically make no difference. If you switch, say, valine for isoleucine, most of the time it's not going to hurt much (or help much.) (The reason our mutant animals have something wrong with them is that we're trying to mimic a diseased human; if they weren't defective, we wouldn't be interested.)

Billions of years of evolution have honed things down pretty well. If a protein gets altered, it's a lot easier to have a sudden loss of function than it is to have a sudden gain. It's like popping your hood and throwing rocks at your car engine - you have a better chance of damaging the thing than you have of whacking it in a way that increases your gas mileage.

I wrote about a particularly vivid example of this a couple of years ago on my old Lagniappe site. (That material seems to be succumbing to bit-rot when I try to pull it out via Google, so I'm going to rescue some of it every so often.) Here's a slightly reworked version of what I had to say about a famous Alzheimer's mutation:

One of the things that gives me the willies about biochemistry is the nonlinearity. If anyone were to ever come up with a set of equations to model all the ins and outs ofa living organism, there would be all these terms - way out in the boonies of the expression - with things to the eighth and tenth powers in them.

Of course, the coefficients in front of those terms would usually be zero, or close to it, so you'd hardly know they were out there. But if anything tips over and gives a little weight to that part of the equation. . .suddenly something unexpected wakes up, and a buried biological effect comes roaring to life out of nowhere.

Here's the real-world example that got me thinking in that direction. When I used to work on Alzheimer's disease, I first learned the canonical Amyloid Hypothesis of the disease. Briefly put, at autopsy, the brains of Alzheimer's patients always show plaques of precipitated protein, surrounded by dying neurons. It's always the same protein, a 42-amino-acid number called beta-amyloid. A good deal of work went into finding out where it came from, namely, from a much larger protein (751 amino acids) called APP. That stands for "amyloid precursor protein," in case you thought that acronym was going to tell you something useful

The ever-tempting hypothesis has been that an abnormal accumulation of beta-amyloid is the cause of Alzheimer's. This isn't the time to get into the competing hypotheses, but amyloid has always led the pack, notwithstanding a vocal group of detractors who've claimed that Alzheimer's gives you amyloid deposits, not the other way around. (Note from 2004: I wrote recently about developments in the amyloid field here and here.)

So what's APP, and what's it good for? It took all of the 1990s to answer that one, and the answers are still coming in. It's found all over the place, and seems to have a role in cellular (and nuclear) signaling. Normally, it's cleaved to give smaller protein fragments other than the 42-mer that causes all the trouble.

One of the stronger arguments for amyloid as an Alzheimer's cause came from the so-called "Dutch mutation," which is what got me to thinking. As was worked out in 1990, there's a family in Holland with a slightly different version of APP. One of the 751 amino acids is changed - where the rest of the world has glutamic acid, they have glutamine - almost the same size and shape, but lacking the acidic side chain.

So. . .there's one amino acid out of 751 that's been altered. And that's in one protein out of. . .how many? A few hundred thousand seems like the right order of magnitude for the proteome, maybe more. And what happens if you kick over that particular grain of sand on the beach? Well, what happens is, you die - with rampaging early-onset Alzheimer's (and a high likelihood of cerebral hemorrhage) before you're well into your 40s.

As it happens, that amino acid is right in the section of the protein that becomes beta-amyloid. Altering it makes it much easier for proteases to come and break the amide bond in the protein backbone, so you start accumulating beta-amyloid plaques early. Much too early. Bad luck - the change of just a few atoms - snowballs into metabolic disaster. Since then, many other mutations have been found in APP, and many of them are bad news for similar reasons.

But it's not like every amino acid substitution in some random protein causes death, of course. There are any number of silent mutations, and plenty that are relatively benign. Most of the time, those high-exponent terms out there in the mathematics sleep on undisturbed. And it's better that way.

Research, The Right Way

For today, instead of reading something over here, I'd like to send everyone over to Australian physicist Michael Nielsen. He's been writing a manifesto about how to do research, and here's the finished product. (Thanks to Chad Orzel for the link.)

I find his prespective to be very accurate indeed. Readers may recognize some themes that I've sounded over here from time to time. I'll be add my own comments in a future post or two.

Furry Judges, With Tails

The phrase "guinea pig" entered the language a long time ago as slang for "test animal", but I've yet to make a compound that's crossed a guinea pig's lips. Guinea pigs are still used for a few special applications, but since the beginning of my career, I've been surrounded (metaphorically!) by rats and mice.

Of the two, I prefer the mice. That's probably because they're smaller, and need correspondingly less effort from people like me to make enough drugs to dose them. The animal-handling folks prefer them for similar reasons: rats are more ornery, and they can fetch you a pretty useful bite if they're in the mood. When I was working in Alzheimer's disease, we had a small group of elderly rats that we were checking for memory problems. If that makes you think of rat-sized rocking chairs, think again. These were big ugly customers, feisty, wily critters that knew all the tricks and were no fun to deal with. Give me mice any day.

Of course, there are mice and there are mice. "Wild-type" mice are pretty hearty, but we don't use rodents captured out in the meadow. They're too variable, not to mention being loaded down with all sorts of interesting diseases. Every rodent we use in the drug industry comes from one of the big supply houses. Even our wild-types are a particular strain, identified with a catchy moniker like "K57 Black Swiss."

You're in good shape if you can use regular animals for your drug efficacy tests, but we often work on diseases which have no good rodent equivalents. People in diabetes projects, for example, often use mutant mice such as the db/db and ob/ob strains, which are genetically predisposed to put on weight. Eventually they can show some (but not all) of the signs of Type II diabetes. They can get pretty hefty - you'd better plan on making more compound if you're going to be testing things in those guys. Meanwhile, cancer researchers go through huge number of the so-called nude mice, a nearly hairless mutant variety with a compromised immune system. You've got to know what you're doing when you have a big group of those guys, because you can imagine how a contagious rodent disease could tear through them.

All the mutant animal lines are damaged in one form or another, since they're supposed to serve as a model of a disease. (Actually, most mutants in any animal population are damaged, since in a living system it's a lot easier to make a random change for the worse than it is to make one for the better.) They're just not as robust as the wild types. They need special handling, and they can't tolerate all the methods of compound dosing that a normal animal can. In some cases, you're restricted to the mildest, tamest vehicle solutions. (You know, the ones you can't get any of your compounds to go into.)

And there's always that nagging doubt about how valid your animal models might be. Some research areas have worked out a pretty good correlation between what works in people and what works in mice, but many of us are still stumbling around. The more innovative your work, the less of an idea you have about whether you're wasting your time. 'Twas ever thus.

John Kerry on Drug Prices

I didn't watch John Kerry's speech tonight. I'll watch a political speech made to a potentially hostile or sceptical audience (like the State of the Union) but not one made to an adoring throng, either throng. Life is too short.

But I've had some e-mail pointing out that Kerry whipped out a line about drug prices, which I presume was an applause-getter:

"Under our plan, Medicare will negotiate lower drug prices for seniors. And all Americans will be able to buy less expensive prescription drugs from countries like Canada."

Of course, the law as it stands forbids any drug company from offering anyone a lower price than they offer Medicare. Ask Schering-Plough how that one works. But what Kerry is talking about is modifying the latest Medicare drug benefit, to allow the federal government to directly negotiate drug prices. My industry put up a serious battle to keep that from happening, and it's no secret why. This is a direct route to Federally mandated drug price controls. If you think that those are a good thing, then you like that idea - if not, you don't.

And as for importing drugs from Canada, well, I'll resist the temptation to start turning purple again. But I took Kerry's suggestion to go to his campaign website for more details:

"The Kerry-Edwards plan will reduce prescription drug prices by allowing the re-importation of safe prescription drugs from Canada, overhauling the Medicare drug plan, ensuring low-cost drugs, and ending artificial barriers to generic drug competition."

Now that word "safe" is an interesting one to drop in there. As many readers know, Congress has already passed a law making it legal to reimport drugs from Canada - but only if the FDA certifies their safety. And that the agency has refused to do, saying they don't have the resources to make such a guarantee. Is Kerry planning to give the FDA whatever it might need to go ahead and make the call? Or is this an escape clause to allow the status quo to prevail?

Well, if that Medicare idea comes true, it could be a moot point. There won't be much need to import drugs from Canada if we become Canada, will there?

Down in the Salt Mine

As I mentioned yesterday, I've been spending the last couple of days working on salt forms of one of our compounds. Even folks who slept through one semester of general chemistry may remember that an acid plus a base gives you a salt, which is just what I've been doing. Most of the compounds we work with have a basic nitrogen atom in them somewhere - medicinal chemistry would grind to a halt without basic nitrogens - so to form a salt you add an equivalent amount of some acid.

Once or twice in my career I've batted from the other side of the plate, working with acidic compounds and making a salt by adding a base. There are some therapeutic targets where only acidic compounds seem to work, but I haven't spent as much time on those. Actually, acidic compounds aren't as much trouble. They seem to behave a little better in their original form than the strongly basic ones do, partly because they're not suddenly being jerked over to the other end of the pH scale when they hit the stomach, and partly because they can deal with a whole different set of uptake and transport systems.

The reason you go to all this salt trouble is because the salts are often easier to dissolve and dose than the free bases. Often the situation is even worse than that: the free base is nearly impossible to dose, and a salt form is your only way out. There are a limited number of things you can dissolve your compound in if you're giving it to a mouse or rat every day. (The rats are a bit more resilient, as a rule.) Water would be ideal, but I'm not sure if I've made half a dozen things in the last fifteen years that would just dissolve in straight water.

A common (and reasonably innocuous) additive is polyethylene glycol, known in the trade just as "peg." (I often come away from formulation discussion humming Steely Dan.) I'm trying to get these compounds into half-and-half PEG/water, and anything will be an improvement over the lumpy-gravy suspensions that we're getting now. Suspensions aren't bad per se: a good one, which has the pearly look of an opaque shampoo, is a fine dosing method. But they're not all created equal, and they're harder to generate reproducibly. The problem with dosing the oatmealy ones is that they give you lower blood levels than you expect for a given amount of compound, and the levels tend to vary along with the (unreproducible) size of the lumps. The experiments are nearly worthless.

So what sorts of acids do we use? The most popular is good ol' hydrochloric. At least half the pharmaceutical salts on the market are HCl-derived. Then there are salts from organic acids (maleate, citrate, fumarate, gluconate), other mineral acids (sulfate, phosphate), and some mixed breeds like methanesulfonate. Those probably cover 95% of what's out there.

The ideal salt is stable, powdery, free-flowing, and doesn't turn into a goo by soaking up water from the air. You find that elegant substance in the least elegant way possible, because there is absolutely no way to tell which of these is going to be the best. There are some rank-order decision tree charts that people use, but they're departed from as often as they're honored. My chosen field, once you get the gift wrap off of it, is about as empirical as they come.

A Question For the Audience

You know, it does feel odd not to be writing anything about the political season, what with all the conventioneering going on. But world events, for the most part, sort of wash over and around this blog, which is a decision I made back in my early days. Political opinions are piling up unsold in every market stall, but who offers commentary on chemistry?

Of course, there's always the question of market size. A single-subject site is never going to pull in the traffic of the big generalist ones, unless the subject is something rather more stimulating than organic chemistry (if you know what I mean and I think you do, as Joe Bob Briggs used to say.) But I've been encouraged by the responses I've had from people completely outside the sciences who've enjoyed visiting them by reading here.

Still, knowing that I have a widely mixed audience makes it tricky sometimes. There are some subjects that are harder to cover, and there are jokes that are hard to make. For example, I guarantee that every organic chemist will at least smile at a phrase like, oh, "plutonium enolate." But that's not going to make 'em spill their beer down at the comedy club, unless they're spilling it on the person trying to tell the joke.

So I'd like to take advantage of this slow news period to ask people if there are topics they'd like to see more (or less) of: current pharma news, stock market stuff, lab stories, med-chem background, purple-faced rants about price controls? Comment below, or feel free to e-mail me.

I hesitate to mention topics that I'm planning to post on, because it seems that I never get around to them, but the future should hold pieces on combination drugs (boon or gimmick?), salts and why I'm making a bunch of them right now, and (if I can summon the energy) a whack at Martha Angell and her recent NY Review of Books broadside against my industry. She has a book coming out this fall, and naturally I can hardly keep my enthusiasm from just foaming up all over the place. Sheesh.

How Long Can This Go On?

Back before my vacation, I mentioned the problem of judging how long a drug project should be allowed to run. You have to call a halt eventually, because it's very rare for a project to finish of its own accord - by which I mean "arrive at a conclusion that no one can argue about or wish to change."

That goes for either kind of conclusion. It's difficult for a project to fail so conclusively that no one wants to take just one more crack at it. Maybe you haven't been dosing the right way, or in the right formulation, or in the right sort of animal. There's always another series of compounds to try; success could be just around the ol' corner. Sometimes it is - there are some tremendously successful drugs that nearly died several times in preclinical development, until someone found a way to defibrillate the project and make it get off the floor.

I have managed to totally kill one at least once in my career, though, when we showed that there was an insurmountable side effect problem caused by the exact same enzyme that we were already targeting. Turns out that it does two different things in different tissues, and any inhibitor is thus going to run into the same problem. Not a thing you can do about it.

And on the successful side, it's unusual for a compound to do everything you want it to - potent, selective, good oral dosing, no side effects, cheap and easy to make on large scale. Most of the time, you're faced with an array of compounds, each of which might do the job, each with a different pattern of potential defects. If you'll only accept a perfect compound, you'll spend years crawling up the asymptotic curve, spending ever more money to fix ever smaller problems. You just have to call a halt at some point and declare that what you have is good enough. (This is no doubt sounding very familiar to the engineers out there.)

But when do you reach that point? I wish I had a general answer. (If I had one, I'd probably be writing this from my private island estate.) Clearly, for a bigger potential payoff you should be willing to spend more money and take more time. A potential breakthrough therapy should get several chances to come back from the grave, which is why (as I mentioned above) there's a disproportionate number of such stories among the blockbuster drugs.

But having your project nearly die doesn't mean that it's going to be a winner; that's not how you join that club. The sixth-on-the-market therapy for toenail fungus could just as easily be an exciting development story for those involved; it doesn't mean that it was worth doing.

How Not to Do It: Sulfenyl Chlorides

Someone came to my lab today to borrow some thiophenol, a request that made me think of something that happened in my first summer of undergraduate research - twenty-two, gulp, years ago. Now, thiophenol is not known as a great inducer of nostalgia. Like the other small-molecule sulfur compounds, it reeks without letup. It's a major part of the smell of burning rubber, so if you can imagine that concentrated and put into a bottle, you've got a pretty good idea. It's distinctive.

I was using this cologne as a starting material, reacting it with sulfuryl chloride, which is another reagent that no one is going to dab behind their ears. It's a reactive chlorinating agent and a fairly strong oxidizer, and it'll make you shake your head and snort if you come across its fumes, for sure. The two of them together make an eyebrow-raising mixture - I was exiled to a lab at the other end of the building while I ran this one, just because of the potential smells.

Heating this brew gives you phenylsulfenyl chloride, a red oil which combines the foul properties of its parent compounds. You distill the stuff out of the reaction, cap it up, and store it in the cold. I think it's too reactive to be an article of commerce; you have to make it fresh. And make it fresh I did, even though everything around me smelled as it had been dead for weeks. In the freezer with the stuff for the weekend (we didn't work grad-school hours at my all-undergraduate school, not even in these summer research programs.)

Monday morning I went down and picked up the flask. Hmmm. . .no longer a red oil. Odd. The stuff had changed to a pale yellow solid, which didn't seem right. I wasn't sure of the compound's freezing point, but the color change alone made me wonder. I stood there puzzled for a minute or so with the tightly stoppered flask in my hand, holding it up to see what I could make of the stuff. And then, with a loud gunshot bang, the top of the flask exploded in my hand.

I jumped straight up in the air, flinging away the lower part of the flask that I was still holding. I came down on the balls of my feet, in a fight-or-flight stance, looking around wildly. I didn't feel as if I'd been injured, but I'd never had anything blow up while I was holding it, either, so who kenw? After a second or so I looked down to see if I was OK. And weirdly enough, I was. I can't imagine how I managed not to pick up some glass shrapnel, at least - perhaps even at that early point in my career I had enough sense not to point the neck of a round-bottom flask toward me. My hand was fine - I kept flexing my fingers in wonderment. After a minute of two of stalking around the room, shaking and gibbering, I started looking around to see what had become of the chemical.

I found it about ten feet away, a lens-shaped piece of light yellow stuff, molded smooth by the inside of the flask. Whatever it was, it wasn't melting again, and it sure wasn't phenylsulfenyl chloride. We figured out what it was pretty quickly, but I think I'll leave its identity as an exercise for the technical portion of my readership - guesses to go in the comments below. If you get it right, you'll know why it blew up, too!

Costs and Benefits, Risks and Rewards

Continuing on the latest issue of the New England Journal of Medicine and its articles on cancer therapies, there's the Perspective article, from Deborah Schrag at Sloan-Kettering, which points out that:

"In the wake of the optimism generated by recent trial results, patients experience sticker shock when they encounter the prices of chemotherapy drugs. Physicians find themselves in the undesirable position of having to help patients make decisions about whether the potential clinical benefits warrant the financial strain that even the copayments for these medications may create."

I don't doubt it. She has a chart for a typical patient's eight-week therapy on various regimes. Drug costs for the classic fluorouracil-based therapies will run from $60 to $300 for that period. Throw in irinotecan, the standard since the mid-1990s, and you're looking at about $10,000 for the same eight weeks. An Avastin-based treatment will double that, and an Erbitux-based one will triple it. And those are just wholesale drug costs; they neglect support, labor, wastage, and so on. Avastin and Erbitux are harder to store and administer, so their costs will be still higher. And even if you take the statistics in the latest paper at face value, median survival is increased by less than two months with Erbitux. That brings us to a terrible question: how much are those two extra months worth, and who should pay for them? Everyone's trying to offload that decision onto someone else, and I don't blame them a bit.

We're back to where I was discussing this issue a few weeks ago. As I said then, I think that the solution is that many people won't (and shouldn't) take these therapies, because they're just not worth it. But that's a hard thing to convince someone of, and I'm glad that I don't have to try. My attempt to pass the buck is to point out that none of us in the industry is trying to develop a hugely expensive drug that only prolongs survival by a couple of months - that's just how the damn things come out after we've already spent the time and money. We're trying to hit home runs over here, but the pitching is too strong for us.

The article gets its shots in at the drug industry, though:

"Early scientific work that led to the discovery of bevacizumab (Avastin) and cetuximab (Erbitux) was financed with federal dollars. The pharmaceutical industry translated these fundamental insights into the development of commercial products. The rising stock prices of the publicly traded companies that manufacture these drugs reveal that, development costs notwithstanding, the risk-adjusted return on pharmaceutical products is very high indeed. The drug costs that support these stock prices threaten to overwhelm our ability to pay for health care."

Well. . .let's dispose of those in order, then. The first part is the old drug-companies-rip-off-NIH canard. Allow me to point out that no academic labs were attempting to turn antibodies against the growth factors receptors into new drugs, so why is industry to blame for trying? "Translating fundamental insights into the development of commercial products" is exactly what the drug industry does. It's very hard to do, it's very risky, and it costs a hell of a lot of money. You have a problem with that? If Dr. Schrag believes that she can do it more cheaply and efficiently, I invite her to raise the money and come on down and try it. Many people have done just that, and it's an education, all right.

And as for drug costs overwhelming "our ability to pay for health care", has Dr. Schrag considered that the total contibution of drug costs to health care is below 20%? Isn't there any overwhelming being down by the rest of the business, or are they just standing around in awe of our mighty powers?

And let's see. . .the rising price of the stocks, yes. Please note that I think that Imclone's stock is already too high. As high as Erbitux's cost is, I still don't think it can support Imclone's current price. I think that Bristol-Meyers Squibb overpaid for their share of the drug, and I'm not sure they're going to end up with much of a return. Note also this post about the amount of money that the biotechs have lost over the years - on average, biotech investors have lost money and they continue to lose it. For some years now, anyone investing in the stocks of companies I've worked for has been taking a bracing bath indeed. Believe me, although there are some good investment opportunities, the drug industry only looks like a money machine to the unwary.

Another Shot Across the Bow

Since I last wrote about Imclone, the stock has had a rather difficult time. That's largely the fault of the Imclone fan club: Erbitux sales have exceeded some of the responsible projections, but still haven't caught up with the fantasies of some of the stockholders.

And now comes a study in the New England Journal of Medicine (about as high-profile a place as you can publish this kind of thing) confirming that Erbitux does shows activity in late-stage colon cancer, when added to the standard irinotecan therapy. Good news, eh? But in the end, the publication may do as much harm as good to Erbitux's prospects, because the same issue has a rather sceptical editorial comment on the study, and a longer perspective piece on the costs of such treatments in general. (Full text isn't available to nonsubscribers - the beginning of the editorial is here and the beginning of the Perspective is here. I'm going to cover that one in the next post for Monday; it makes this one too long and unwieldy when they're combined.)

The editorial, from two physicians at the Mayo Clinic, isn't kind. It's enough to make you wonder why they accepted the study for publication in the first place: ". . .the findings clearly support the notion that interfering with EGFR signaling can overcome the resistance to irinotecan. Nevertheless, the appropriateness of the authors' reporting methods warrants discussion." They point out that the trial was statistically underpowered to detect some clinically meaningful differences, and question whether the reported response rate can justify using Erbitux as a monotherapy. The authors attempted to test the patients for EGFR expression, but it's unclear if they did this in the right way (it's not as simple as you'd think.)

Even if you take the statistics as they are, Erbitux added less than two months to the lives of patients, on average, compared to the current standard of care. The authors' verdict: there may well be clinical settings or treatment regimens where Erbitux is more useful in such colon cancer patients, but we don't know what they are yet. The addition of Erbitux to the list of treatments, they say, "must be tempered by the small advances that it offers in terms of the time to progression and the response rate and its uncertain effects on survival. . ." Not to mention the cost, which we'll take up in the next post.

In light of all this, I'd like to take a moment to address the Imclone-boosting stock cult, those few of them who might have read this far, anyway. Get out. Take the money and run. The alarm bell has sounded, and more than once. If you bought Imclone when it was in the dumper, you've had a great run. Celebrate and cash in! But if you bought it when I was ranting on the subject back in late June, you're in the red, and I fear that it's going to be even worse in the long run. Flee!

Worries about Rimonabant?

Continuing on the theme of unexpected toxicity landmines, I wanted to take a look at a highly anticipated obesity drug from Sanofi. Rimonabant is a small molecule antagonist of the CB-1 receptor, and it's been getting a lot of press - both for its impressive efficacy and for its mechanism of action. The "CB" in the receptor name stands for "cannabinoid", and the drug blocks the same receptor whose stimulation causes the well-known food cravings brought on by marijuana.

Interestingly, blockade of this receptor not only seems to affect appetite, but also seems to help with cravings for nicotine. As you can imagine, the market potential for the drug could be immense (and as you can imagine, other drug companies are chasing the same biological target, too.)

But what else does an antagonist do? The receptor has, no doubt, several functions in the brain (all the CNS receptors do multiple duty), and it's scattered around in the nerves and other tissues as well. There have been a couple of reports that bear watching. A team of researchers (German/Italian/US) reported earlier this year that the CB-1 receptor seems to be involved in inflammation of the colon. Mice with the receptor knocked out show great susceptibility to chemical irritants in the gut, and (more disturbingly) the same effect was seen in normal mice treated with a CB-1 antagonist. The authors suggest that CB-1 may be involved in diseases like Crohn's and irritable bowel syndrome, but antagonists would, if anything, make the problem worse.

That's bad enough, but there's a potential disaster that just showed up last month. The authors report that a patient of theirs suddenly came down with multiple sclerosis after having been a subject in a rimonabant trial. Now, there's no way to prove causation, as they freely admit, but there's some evidence that CB-1 has a neuroprotective effect under normal conditions. So blocking its actions might conceivably expose neurons to damage, and when you combine that with the above potential role in inflammation, you have something that you should keep an eye on.

No one can say how this will play out. The most likely outcome is the best one - that the drug isn't associated with MS or Crohn's. After all, it's been through some extensive trials, and Sanofi still seems confident - which, believe me, they wouldn't be if a good fraction of the participants had come down with irritable bowel syndrome, much less multiple sclerosis. But there's another possibility, that the trouble will only show up in some patients under some conditions, and it might be rare enough that you won't see it until it gets out into the general population. There's just no way to run a clinical trial to nail down the statistics on, say, a one in 50,000 side effect. You'll never see it coming.

That MS report in particular must have the Sanofi people a bit worried, and I'm sure it has the attention of the other players in the area, who will be glad to let Sanofi go out and be the lightning rod in case anything bad happens. Odds are that it won't, but there are no sure things, not with this drug or any other. Honestly, it's years before you can relax in this business, if you ever do. Good luck, guys.

Bungee Jumping with PPAR Drugs

The PPAR family (known in the US as alpha, gamma, and delta, for obscure historical reasons) is one of those biological jungles that keep us all employed. They're nuclear receptors, and thus they're involved in up- and down-regulation of hundreds of genes. Like most of the other nuclear receptors, they do that by responding to small molecules, which makes the whole class a unique opportunity for medicinal chemists.

Normally, we can't do much about gene regulation, because it's all handled by huge multicomponent protein complexes, terrible and unlikely candidates for intervention with our drug molecules. But when the whole thing is set off by binding of a small ligand, well, that's all the invitation we need. To pick a well-known class of small ligands, the best-known members of the NR superfamily are the steroid receptors, which should give you some idea of how powerful these things can be.

For their part, the PPARs are all major players in cellular energy balance and fuel use, the handling of fatty acids and other lipids, the generation and remodeling of adipose tissue, and similar things. That lands them squarely in some very important therapeutic areas such as diabetes, obesity, and cardiovascular disease. But more recently, it's become clear that they're also involved in things like inflammation and carcinogenesis, which brings in another huge swath of the drug industry. Every large drug company is working on them, for one indication or another. Heck, you could run an entire drug company on nothing but PPAR-related targets, that is, if you weren't terrified by the insane risk that you were taking.

Problem is, the biology of nuclear receptors is powerfully complex and murky. We know a lot more about them than we did five or ten years ago, but it's obvious to everyone in the field that we still have very little idea of what we're doing. Take a look at the three PPARs: there are two diabetes drugs on the market that target PPAR gamma (Avandia and Actos, aka rosiglitazone and pioglitazone), but no one has been able to get anything significantly better or safer than either of those. PPAR alpha is supposed to be the way an old class of lipid lowering drugs (the fibrates) work, but no one's really sure that they believe that. Several companies have been working on PPAR alpha drugs for a long time now, and nothing's made it deep into the clinic yet, which isn't a good sign. And no one really knows what PPAR delta does - it seems to have something to do with lipid levels, and something to do with wound healing, and something to do with colon cancer. The clues are rather widely scattered.

I've mentioned that several companies have been working on combination diabetes drugs that would hit both PPAR gamma and alpha. The idea is that they'd do all the glucose lowering of a gamma-targeted drug, and lower lipid levels at the same time - a worthy goal for the typical overweight Type II diabetic patient. But Novo Nordisk, racing along with a compound they licensed from India's Dr. Reddy's (the evocatively named ragaglitazar) hit the banana peel when long-term rodent testing showed that the compound was associated with bladder cancer. Then Merck, which had a compound from Japan's Kyorin in advanced trials, pulled it when another rare cancer showed up in long-term rodent studies. Screeching halt, all over the industry.

Now the FDA has jumped in, with a requirement that any new PPAR drugs go through two-year rodent toxicity testing. That's an unusual requirement, but (as the two examples above show) it's something that companies were already doing on their own initiative. Bristol-Meyers Squibb and AstraZeneca have already done theirs, for example, and are plowing on.

The feeling has been: no one really knows what to expect from new PPAR compounds, so you'd better test the waters extensively. The thought of putting a compound on the market that turns out - years later - to be linked to increased risk of something like bladder cancer is enough to give everyone nightmares. I should mention that nothing bad has been seen from the two marketed PPAR gamma compounds I mentioned. But everyone remembers that there was another one, troglitazone, the first to market and the first to be pulled. It showed liver toxicity, but that seems to have been compound-related rather than mechanism-related.

Here's an article from Forbes on the subject, one of the few outlets that covered this story in any detail. It's pretty good, although it glosses over a lot of things. For example, the article quotes Ralph DeFronzo of UT-San Antonio saying that the fibrate drugs have been targeting PPAR-alpha for years, so why is the FDA worried about that subtype? What that ignores is that the fibrates are actually very weak drugs at alpha, which is why I mentioned the doubts people have about the whole mechanism. The drugs being developed now are thousands of times more potent. And look at the alpha-gamma combinations: why did all the trouble start only when alpha was added to the mix?

Well, we've got plenty of work to do. Unraveling the biological effects of the PPARs is going to take many, many years. And we're going to have to do it in rodents, in dogs, and in humans, at the very least - all the major species that are tested for toxicity. We already know about some significant differences between the species in the way that these nuclear receptors work. Will these cancer problems be another one? Are humans going to be just fine? Or will we react in even worse ways, given enough time? We just don't know. Everyone's holding their breath, waiting to see what comes next. . .

Back for More

I've spaded through the heap of e-mail at home and at work, and I'm ready to get going again. My lab is on another new project, which means that I need to clear my desk of the piles of notes and papers from the last one. Some of those will go into the permanent files, while others will go into the handy recycling box. Rather more of the latter, actually.

Here comes another class of molecules that I've never worked on before, but to judge from the torrent of hits that I get from literature searches, they've had plenty of admirers. It's the exact situation I spoke about recently: we've got to carve out some patent space and hope that it overlaps with the space of active compounds. There are whole classes of structures that we're probably not even going to bother looking at, because it's clear that we can't own a position there.

Really significant effort goes into such contortions. I can't imagine what a pharmaceutical world without chemical intellectual property would feel like, but it sure would be less complex for people like me. Mere anarchy would sure enough be loosed: just make whatever you want to, and go where the assays tell you. But I can't imagine how you'd make it pay, either, which is why we're in the world we're in.