Corante

About this Author
DBL%20Hendrix%20small.png College chemistry, 1983

Derek Lowe The 2002 Model

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

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

Chemistry and Drug Data: Drugbank
Emolecules
ChemSpider
Chempedia Lab
Synthetic Pages
Organic Chemistry Portal
PubChem
Not Voodoo
DailyMed
Druglib
Clinicaltrials.gov

Chemistry and Pharma Blogs:
Org Prep Daily
The Haystack
Kilomentor
A New Merck, Reviewed
Liberal Arts Chemistry
Electron Pusher
All Things Metathesis
C&E News Blogs
Chemiotics II
Chemical Space
Noel O'Blog
In Vivo Blog
Terra Sigilatta
BBSRC/Douglas Kell
ChemBark
Realizations in Biostatistics
Chemjobber
Pharmalot
ChemSpider Blog
Pharmagossip
Med-Chemist
Organic Chem - Education & Industry
Pharma Strategy Blog
No Name No Slogan
Practical Fragments
SimBioSys
The Curious Wavefunction
Natural Product Man
Fragment Literature
Chemistry World Blog
Synthetic Nature
Chemistry Blog
Synthesizing Ideas
Business|Bytes|Genes|Molecules
Eye on FDA
Chemical Forums
Depth-First
Symyx Blog
Sceptical Chymist
Lamentations on Chemistry
Computational Organic Chemistry
Mining Drugs
Henry Rzepa


Science Blogs and News:
Bad Science
The Loom
Uncertain Principles
Fierce Biotech
Blogs for Industry
Omics! Omics!
Young Female Scientist
Notional Slurry
Nobel Intent
SciTech Daily
Science Blog
FuturePundit
Aetiology
Gene Expression (I)
Gene Expression (II)
Sciencebase
Pharyngula
Adventures in Ethics and Science
Transterrestrial Musings
Slashdot Science
Cosmic Variance
Biology News Net


Medical Blogs
DB's Medical Rants
Science-Based Medicine
GruntDoc
Respectful Insolence
Diabetes Mine


Economics and Business
Marginal Revolution
The Volokh Conspiracy
Knowledge Problem


Politics / Current Events
Virginia Postrel
Instapundit
Belmont Club
Mickey Kaus


Belles Lettres
Uncouth Reflections
Arts and Letters Daily

In the Pipeline

Category Archives

« Snake Oil | The Central Nervous System | The Dark Side »

July 22, 2014

The Broad Gets $650 Million For Psychiatric Research

Email This Entry

Posted by Derek

The Broad Institute seems to have gone through a bit of rough funding patch some months ago, but things are looking up: they've received a gift of $650 million to do basic research in psychiatric disorders. Believe it, that'll keep everyone busy, for sure.

I enjoyed Eric Lander's characterization of much of the 1990s work on the genetic basis of mental illness as "pretty much completely useless", and I don't disagree one bit. His challenge, as he and the rest of the folks at the Broad well know, is to keep someone from being able to say that about them in the year 2034. CNS work is the ultimate black box, which makes a person nervous, but on the other hand, anything solid that gets discovered will be a real advance. Good luck to them.

You might also be interested to know where the Stanley Foundation, the benefactors here, came up with over half a billion dollars to donate to basic medical research (and more to come, apparently). You'd never guess: selling collectibles. Sports figurines. Small replicas of classic cars, trucks, and tractors. Miniature porcelain versions of popular dolls. Leather-bound sets of great (public domain) novels. Order now for the complete set of Presidential Coins - that sort of thing. It looks to be a lot more lucrative than discovering drugs (!)

Comments (49) + TrackBacks (0) | Category: General Scientific News | The Central Nervous System

June 3, 2014

Alex Shulgin, 1925-2014

Email This Entry

Posted by Derek

Alex (Sasha) Shulgin has died at the age of 88. Among some groups of people, he was the most famous chemist in the world - I refer specifically to people with a strong interest in psychedelic drugs. Shulgin was, of course, the author of PIHKAL and TIHKAL, books whose titles resolve to, respectively, Phenethylamines/Tryptamines I Have Known And Loved, which should tell you where he was coming from.

But his days were different from these days. When Shulgin was doing his earlier work, these compounds were (for the most part) not illegal. Even after their legal status changed, Shulgin had cordial relations with the DEA (up until the early 1990s, that is, when things went downhill). He was certainly not interested in becoming a drug lord, or coming up with the most efficient backyard synthesis of some profitable amphetamine. Shulgin was interested in the human brain and what happened to it when you messed around with its balance of neurotransmitters, and he was his own test subject (along with a circle of friends). The papers he published on this work read now like documents from another planet - there in the Journal of Organic Chemistry would be a paper on the SAR of some series of compounds, with an experimental section that looked normal until you got to the in vivo part. It would read something like "Six subjects with experience in psychoactive substances ingested doses ranging from. . .", and it would go on to detail their responses on the Shulgin Rating Scale. (A complete publication list can be found at Shulgin's Wikipedia entry).

He actually inspired a number of people to become organic chemists. I wasn't one of them (I didn't hear about him until I was already in grad school), but I do know of others. And even though I'm about as far from him as possible in my willingness to experiment with psychoactive substances (never touched any, never plan to), I always had a lot of sympathy for him. He wanted to find out what such things did, and he was willing to do what it took to find out. We disagree in philosophy as well - Shulgin felt (as have many people who've experienced such compounds) that they provided a window into a more complicated reality. I don't put much stock in that myself - it seems to me like hearing a snarl of static after pouring a cup of coffee into the back of a radio and then deciding that it was a new kind of radio station. I think that exposing oneself to these agents risks brain damage, and since I discount the experiences they provide, it's never seemed worthwhile to me. But never having taken any such substances myself, I realize that my authority to speak about them may be limited. Many people seem to have benefited from exposure to psychedelics, while others appear to have been permanently damaged. An inability to tell which group I might fall into does not increase my desire to try anything in this line, either.

Shulgin was a very unusual person, but he was also a pioneer and a real scientist. If he has imitators, psychedelic self-experimenters who are not interested in making money, they're keeping quiet. Instead, we have plenty of folks who don't mind experimenting on others, as long as the money comes in. Many of these people probably see themselves as Shulgin's heirs, and I wonder if he thought of them as such or not. Risking your own neurons in your isolated farmhouse can be plausibly thought of as your own business - selling piles of untested compounds to partygoers is (at least to me) a different matter.

Comments (44) + TrackBacks (0) | Category: Chemical News | The Central Nervous System

April 8, 2014

A Call For Better Mouse Studies

Email This Entry

Posted by Derek

Here's an article by Steve Perrin, at the ALS Therapy Development Institute, and you can tell that he's a pretty frustrated guy. With good reason.
ALS%20chart.png
That chart shows why. Those are attempted replicates of putative ALS drugs, and you can see that there's a bit of a discrepancy here and there. One problem is poorly run mouse studies, and the TDI has been trying to do something about that:

After nearly a decade of validation work, the ALS TDI introduced guidelines that should reduce the number of false positives in preclinical studies and so prevent unwarranted clinical trials. The recommendations, which pertain to other diseases too, include: rigorously assessing animals' physical and biochemical traits in terms of human disease; characterizing when disease symptoms and death occur and being alert to unexpected variation; and creating a mathematical model to aid experimental design, including how many mice must be included in a study. It is astonishing how often such straightforward steps are overlooked. It is hard to find a publication, for example, in which a preclinical animal study is backed by statistical models to minimize experimental noise.

All true, and we'd be a lot better off if such recommendations were followed more often. Crappy animal data is far worse than no animal data at all. But the other part of the problem is that the mouse models of ALS aren't very good:

. . .Mouse models expressing a mutant form of the RNA binding protein TDP43 show hallmark features of ALS: loss of motor neurons, protein aggregation and progressive muscle atrophy.

But further study of these mice revealed key differences. In patients (and in established mouse models), paralysis progresses over time. However, we did not observe this progression in TDP43-mutant mice. Measurements of gait and grip strength showed that their muscle deficits were in fact mild, and post-mortem examination found that the animals died not of progressive muscle atrophy, but of acute bowel obstruction caused by deterioration of smooth muscles in the gut. Although the existing TDP43-mutant mice may be useful for studying drugs' effects on certain disease mechanisms, a drug's ability to extend survival would most probably be irrelevant to people.

A big problem is that the recent emphasis on translational research in academia is going to land many labs right into these problems. As the rest of that Nature article shows, the ways for a mouse study to go wrong are many, various, and subtle. If you don't pay very close attention, and have people who know what to pay attention to, you could be wasting time, money, and animals to generate data that will go on to waste still more of all three. I'd strongly urge anyone doing rodent studies, and especially labs that haven't done or commissioned very many of them before, to read up on these issues in detail. It slows things down, true, and it costs money. But there are worse things.

Comments (19) + TrackBacks (0) | Category: Animal Testing | The Central Nervous System

March 28, 2014

A Huntington's Breakthrough?

Email This Entry

Posted by Derek

Huntington's is a terrible disease. It's the perfect example of how genomics can only take you so far. We've known since 1993 what the gene is that's mutated in the disease, and we know the protein that it codes for (Huntingtin). We even know what seems to be wrong with the protein - it has a repeating chain of glutamines on one end. If your tail of glutamines is less than about 35 repeats, then you're not going to get the disease. If you have 36 to 39 repeats, you are in trouble, and may very well come down with the less severe end of Huntington's. If there are 40 or more, doubt is tragically removed.

So we can tell, with great precision, if someone is going to come down with Huntington's, but we can't do a damn thing about it. That's because despite a great deal of work, we don't really understand the molecular mechanism at work. This mutated gene codes for this defective protein, but we don't know what it is about that protein that causes particular regions of the brain to deteriorate. No one knows what all of Huntingtin's functions are, and not for lack of trying, and multiple attempts to map out its interactions (and determine how they're altered by a too-long N-terminal glutamine tail) have not given a definite answer.

But maybe, as of this week, that's changed. Solomon Snyder's group at Johns Hopkins has a paper out in Nature that suggests an actual mechanism. They believe that mutant Huntingtin binds (inappropriately) a transcription factor called "specificity protein 1", which is known to be a major player in neurons. Among other things, it's responsible for initiating transcription of the gene for an enzyme called cystathionine γ-lyase. That, in turn, is responsible for the last step in cysteine biosynthesis, and put together, all this suggests a brain-specific depletion of cysteine. Update: this could have numerous downstream consequences - this is the pathway that produces hydrogen sulfide, which the Snyder group has shown is an important neurotransmitter (one of several they've discovered), and it's also involved in synthesizing glutathione. Cysteine itself is, of course, often a crucial amino acid in many protein structures as well.)

Snyder is proposing this as the actual mechanism of Huntington's, and they have shown, in human tissue culture and in mouse models of the disease, that supplementation with extra cysteine can stop or reverse the cellular signs of the disease. This is a very plausible theory (it seems to me), and the paper makes a very strong case for it. It should lead to immediate consequences in the clinic, and in the labs researching possible therapies for the disease. And one hopes that it will lead to immediate consequences for Huntington's patients themselves. If I knew someone with the Huntingtin mutation, I believe that I would tell them to waste no time taking cysteine supplements, in the hopes that some of it will reach the brain.

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

March 14, 2014

The Genetics of Bipolar Disorder: What A Tangle

Email This Entry

Posted by Derek

Here's a brave attempt to look for genetic markers of bipolar disorder. The authors studied 388 Old Order Amish sufferers, doing thorough SNP analysis on the lot and total sequencing on fifty of them. There were many parent-child relationships in the set, which gave a chance for further discrimination. And the result:

. . .despite the in-depth genomic characterization of this unique, large and multigenerational pedigree from a genetic isolate, there was no convergence of evidence implicating a particular set of risk loci or common pathways. The striking haplotype and locus heterogeneity we observed has profound implications for the design of studies of bipolar and other related disorders.

If you look around the literature, you'll find numerous smaller studies also trying to find genetic markers for bipolar disorder, and many of these propose possible candidate loci. But very few of them seem to agree, and this new study doesn't seem to confirm any of them. The authors hold out some hope for still larger cohorts and more comprehensive sequencing, and that's certainly the way to go. But if there were anything close to a simple genetic sequence for bipolar disorder, it would have been found by now. Like many other diseases (and not just those of the central nervous system), it's probably a phenotype that can be realized by a whole range of mechanisms, an alternate state of physiology that the system can slip into through a combination of genetic and environmental effects. And while there there may not be a thousand ways to get there, there sure aren't just a couple.

Dealing with these "network diseases" is going to keep us busy for quite a while to come. The best hope, as far as I can see, is for less complexity downstream. Maybe these various susceptibilities and tendencies all slide towards a similar disease process which can be modified. Looking back to the genetic causes for understanding sure hasn't worked out so far; maybe advances in studying brain function and patterns of neurotransmission will shed some light. Although if you're having to look to that area to bail you out. . .

Comments (18) + TrackBacks (0) | Category: The Central Nervous System

December 5, 2013

Parkinson's From the Environment?

Email This Entry

Posted by Derek

I've been meaning to link to this piece by Lauren Wolf in C&E News on the connections between Parkinson's disease and environmental exposure to mitochondrial toxins. (PDF version available here). Links between environmental toxins and disease are drawn all the time, of course, sometimes with very good reason, but often when there seems to be little evidence. In this case, though, since we have the incontrovertible example of MPTP to work from, things have to be taken seriously. Wolf's article is long, detailed, and covers a lot of ground.

The conclusion seems to be that some people may well be genetically more susceptible to such exposures. A lot of people with Parkinson's have never really had much pesticide exposure, and a lot of people who've worked with pesticides never show any signs of Parkinson's. But there could well be a vulnerable population that bridges these two.

Comments (17) + TrackBacks (0) | Category: The Central Nervous System | Toxicology

December 3, 2013

Merck's Drug Development in The New Yorker

Email This Entry

Posted by Derek

The New Yorker has an article about Merck's discovery and development of suvorexant, their orexin inhibitor for insomnia. It also goes into the (not completely reassuring) history of zolpidem (known under the brand name of Ambien), which is the main (and generic) competitor for any new sleep drug.

The piece is pretty accurate about drug research, I have to say:

John Renger, the Merck neuroscientist, has a homemade, mocked-up advertisement for suvorexant pinned to the wall outside his ground-floor office, on a Merck campus in West Point, Pennsylvania. A woman in a darkened room looks unhappily at an alarm clock. It’s 4 a.m. The ad reads, “Restoring Balance.”

The shelves of Renger’s office are filled with small glass trophies. At Merck, these are handed out when chemicals in drug development hit various points on the path to market: they’re celebrations in the face of likely failure. Renger showed me one. Engraved “MK-4305 PCC 2006,” it commemorated the day, seven years ago, when a promising compound was honored with an MK code; it had been cleared for testing on humans. Two years later, MK-4305 became suvorexant. If suvorexant reaches pharmacies, it will have been renamed again—perhaps with three soothing syllables (Valium, Halcion, Ambien).

“We fail so often, even the milestones count for us,” Renger said, laughing. “Think of the number of people who work in the industry. How many get to develop a drug that goes all the way? Probably fewer than ten per cent.”

I well recall when my last company closed up shop - people in one wing were taking those things and lining them up out on a window shelf in the hallway, trying to see how far they could make them reach. Admittedly, they bulked out the lineup with Employee Recognition Awards and Extra Teamwork awards, but there were plenty of oddly shaped clear resin thingies out there, too.

The article also has a good short history of orexin drug development, and it happens just the way I remember it - first, a potential obesity therapy, then sleep disorders (after it was discovered that a strain of narcoleptic dogs lacked functional orexin receptors).

Mignot recently recalled a videoconference that he had with Merck scientists in 1999, a day or two before he published a paper on narcoleptic dogs. (He has never worked for Merck, but at that point he was contemplating a commercial partnership.) When he shared his results, it created an instant commotion, as if he’d “put a foot into an ants’ nest.” Not long afterward, Mignot and his team reported that narcoleptic humans lacked not orexin receptors, like dogs, but orexin itself. In narcoleptic humans, the cells that produce orexin have been destroyed, probably because of an autoimmune response.

Orexin seemed to be essential for fending off sleep, and this changed how one might think of sleep. We know why we eat, drink, and breathe—to keep the internal state of the body adjusted. But sleep is a scientific puzzle. It may enable next-day activity, but that doesn’t explain why rats deprived of sleep don’t just tire; they die, within a couple of weeks. Orexin seemed to turn notions of sleep and arousal upside down. If orexin turns on a light in the brain, then perhaps one could think of dark as the brain’s natural state. “What is sleep?” might be a less profitable question than “What is awake?”

There's also a lot of good coverage of the drug's passage through the FDA, particularly the hearing where the agency and Merck argued about the dose. (The FDA was inclined towards a lower 10-mg tablet, but Merck feared that this wouldn't be enough to be effective in enough patients, and had no desire to launch a drug that would get the reputation of not doing very much).

few weeks later, the F.D.A. wrote to Merck. The letter encouraged the company to revise its application, making ten milligrams the drug’s starting dose. Merck could also include doses of fifteen and twenty milligrams, for people who tried the starting dose and found it unhelpful. This summer, Rick Derrickson designed a ten-milligram tablet: small, round, and green. Several hundred of these tablets now sit on shelves, in rooms set at various temperatures and humidity levels; the tablets are regularly inspected for signs of disintegration.

The F.D.A.’s decision left Merck facing an unusual challenge. In the Phase II trial, this dose of suvorexant had helped to turn off the orexin system in the brains of insomniacs, and it had extended sleep, but its impact didn’t register with users. It worked, but who would notice? Still, suvorexant had a good story—the brain was being targeted in a genuinely innovative way—and pharmaceutical companies are very skilled at selling stories.

Merck has told investors that it intends to seek approval for the new doses next year. I recently asked John Renger how everyday insomniacs would respond to ten milligrams of suvorexant. He responded, “This is a great question.”

There are, naturally, a few shots at the drug industry throughout the article. But it's not like our industry doesn't deserve a few now and then. Overall, it's a good writeup, I'd say, and gets across the later stages of drug development pretty well. The earlier stages are glossed over a bit, by comparison. If the New Yorker would like for me to tell them about those parts sometime, I'm game.

Comments (28) + TrackBacks (0) | Category: Clinical Trials | Drug Development | Drug Industry History | The Central Nervous System

November 8, 2013

Exiting Two Therapeutic Areas

Email This Entry

Posted by Derek

So Bristol-Myers Squibb did indeed re-org itself yesterday, with the loss of about 75 jobs (and the shifting around of 300 more, which will probably result in some job losses as well, since not everyone is going to be able to do that). And they announced that they're getting out of two therapeutic areas, diabetes and neuroscience.

Those would be for very different reasons. Neuro is famously difficult and specialized. There are huge opportunities there, but they're opportunities because no one's been able to do much with them, for a lot of good reasons. Some of the biggest tar pits of drug discovery are to be found there (Alzheimer's, chronic pain), and even the diseases for which we have some treatments are near-total black boxes, mechanistically (schizophrenia, epilepsy and seizures). The animal models are mysterious and often misleading, and the clinical trials for the biggest diseases in this area are well-known to be expensive and tricky to run. You've got your work cut out for you over here.

Meanwhile, the field of diabetes and metabolic disorders is better served. For type I diabetes, the main thing you can do, short of finding ever more precise ways of dosing insulin, is to figure out how to restore islet function and cure it, and that's where all the effort seems to be going. For type II diabetes, which is unfortunately a large market and getting larger all the time, there are a number of therapeutic options. And while there's probably room for still more, the field is getting undeniably a bit crowded. Add that to the very stringent cardiovascular safety requirements, and you're looking at a therapeutic that's not as attractive for new drug development as it was ten or fifteen years ago.

So I can see why a company would get out of these two areas, although it's also easy to think that it's a shame for this to happen. Neuroscience is in a particularly tough spot. The combination of uncertainly and big opportunities would tend to draw a lot of risk-taking startups to the area, but the massive clinical trials needed make it nearly impossible for a small company to get serious traction. So what we've been seeing are startups that, even more than other areas, are focused on getting to the point that a larger company will step in to pay the bills. That's not an abnormal business model, but it has its hazards, chief among them the temptation to run what trials you can with a primary goal of getting shiny numbers (and shiny funding) rather than finding out whether the drug has a more solid chance of working. Semi-delusional Phase II trials are a problem throughout the industry, but more so here.

Comments (58) + TrackBacks (0) | Category: Business and Markets | Diabetes and Obesity | Drug Development | The Central Nervous System

October 29, 2013

Unraveling An Off-Rate

Email This Entry

Posted by Derek

Medicinal chemists talk a lot more about residence time and off rate than they used to. It's become clear that (at least in some cases) a key part of a drug's action is its kinetic behavior, specifically how quickly it leaves its binding site. You'd think that this would correlate well with its potency, but that's not necessarily so. Binding constants are a mix of on- and off-rates, and you can get to the same number by a variety of different means. Only if you're looking at very similar compounds with the same binding modes can you expect the correlation your intuition is telling you about, and even then you don't always get it.

There's a new paper in J. Med. Chem. from a team at Boehringer Ingelheim that takes a detailed look at this effect. The authors are working out the binding to the muscarinic receptor ligand tiotropium, which has been around a long time. (Boehringer's efforts in the muscarinic field have been around a long time, too, come to think of it). Tiotropium binds to the m2 subtype with a Ki of 0.2 nM, and to the m3 subtype with a Ki of 0.1 nM. But the compound has a much slower off rate on the m3 subtype, enough to make it physiologically distinct as an m3 ligand. Tiotropium is better known by its brand name Spiriva, and if its functional selectivity at the m3 receptors in the lungs wasn't pretty tight, it wouldn't be a drug. By carefully modifying its structure and introducing mutations into the receptor, this group hoped to figure out just why it's able to work the way it does.
tiotropium.png
The static details of tiotropium binding are well worked out - in fact, there's a recent X-ray structure, adding to the list of GPCRs that have been investigated by X-ray crystallography. There are plenty of interactions, as those binding constants would suggest:

The orthosteric binding sites of hM3R and hM2R are virtually identical. The positively charged headgroup of the antimuscarinic agent binds to (in the class of amine receptors highly conserved) Asp3.32 (D1483.32) and is surrounded by an aromatic cage consisting of Y1493.33, W5046.48, Y5076.51, Y5307.39, and Y5347.43. In addition to that, the aromatic substructures of the ligands dig into a hydrophobic region close to W2004.57 and the hydroxy groups, together with the ester groups, are bidentally interacting with N5086.52, forming close to optimal double hydrogen bonds. . .

The similarity of these binding sites was brought home to me personally when I was working on making selective antagonists of these myself. (If you want a real challenge, try differentiating m2 and m4). The authors point out, though, and crucially, that if you want to understand how different compounds bind to these receptors, the static pictures you get from X-ray structures are not enough. Homology modeling helps a good deal, but only if you take its results as indicators of dynamic processes, and not just swapping out residues in a framework.

Doing point-by-point single changes in both the tiotropium structure and the the receptor residues lets you use the kinetic data to your advantage. Such similar compounds should have similar modes of dissociation from the binding site. You can then compare off-rates to the binding constants, looking for the ones that deviate from the expected linear relationship. What they find is that the first event when tiotropium leaves the binding site is the opening of the aromatic cage mentioned above. Mutating any of these residues led to a big effect on the off-rate compared to the effect on the binding constant. Mutations further up along the tunnel leading to the binding site behaved in the same way: pretty much identical Ki values, but enhanced off-rates.

These observations, the paper says with commendable honesty, don't help the medicinal chemists all that much in designing compounds with better kinetics. You can imagine finding a compound that takes better advantage of this binding (maybe), but you can also imagine spending a lot of time trying to do that. The interaction with the asapragine at residue 508 is more useful from a drug design standpoint:

Our data provide evidence that the double hydrogen interaction of N5086.52 with tiotropium has a crucial influence on the off-rates beyond its influence on Ki. Mutation of N5086.52 to alanine accelerates the dissociation of tiotropium more than 1 order of magnitude than suggested by the Ki. Consequently, tiotropium derivatives devoid of the interacting hydroxy group show overproportionally short half-lives. Microsecond MD simulations show that this double hydrogen bonded interaction hinders tiotropium from moving into the exit channel by reducing the frequency of tyrosine-lid opening movements. Taken together, our data show that the interaction with N5086.52 is indeed an essential prerequisite for the development of slowly dissociating muscarinic receptor inverse agonists. This hypothesis is corroborated by the a posteriori observation that the only highly conserved substructure of all long-acting antimuscarinic agents currently in clinical development or already on the market is the hydroxy group.

But the extracellular loops also get into the act. The m2 subtype's nearby loop seems to be more flexible than the one in m3, and there's a lysine in the m3 that probably contributes some electrostatic repulsion to the charged tiotropium as it tries to back out of the protein. That's another effect that's hard to take advantage of, since the charged region of the molecule is a key for binding down in the active site, and messing with it would probably not pay dividends.

But there are some good take-aways from this paper. The authors note that the X-ray structure, while valuable, seems to have large confirmed the data generated by mutagenesis (as well it should). So if you're willing to do lots of point mutations, on both your ligand and your protein, you can (in theory) work some of these fine details out. Molecular dynamics simulations would seem to be of help here, too, also in theory. I'd be interested to hear if people can corroborate that with real-world experience.

Comments (20) + TrackBacks (0) | Category: Drug Assays | In Silico | Pharmacokinetics | The Central Nervous System

October 23, 2013

Allosteric Binding Illuminated?

Email This Entry

Posted by Derek

G-protein coupled receptors are one of those areas that I used to think I understood, until I understood them better. These things are very far from being on/off light switches mounted in drywall - they have a lot of different signaling mechanisms, and none of them are simple, either.

One of those that's been known for a long time, but remains quite murky, is allosteric modulation. There are many compounds known that clearly are not binding at the actual ligand site in some types of GPCR, but (equally clearly) can affect their signaling by binding to them somewhere else. So receptors have allosteric sites - but what do they do? And what ligands naturally bind to them (if any)? And by what mechanism does that binding modulate the downstream signaling, and are there effects that we can take advantage of as medicinal chemists? Open questions, all of them.

There's a new paper in Nature that tries to make sense of this, and trying by what might be the most difficult way possible: through computational modeling. Not all that long ago, this might well have been a fool's errand. But we're learning a lot about the details of GPCR structure from the recent X-ray work, and we're also able to handle a lot more computational load than we used to. That's particularly true if we are David Shaw and the D. E. Shaw company, part of the not-all-that-roomy Venn diagram intersection of quantitative Wall Street traders and computational chemists. Shaw has the resources to put together some serious hardware and software, and a team of people to make sure that the processing units get frequent exercise.
shaw%20allosteric.jpg
They're looking at the muscarinic M2 receptor, an old friend of mine for which I produced I-know-not-how-many antagonist candidates about twenty years ago. The allosteric region is up near the surface of the receptor, about 15A from the acetylcholine binding site, and it looks like all the compounds that bind up there do so via cation/pi interactions with aromatic residues in the protein. (That holds true for compounds as diverse as gallamine, alcuronium, and strychnine), and the one shown in the figure. This is very much in line with SAR and mutagenesis results over the years, but there are some key differences. Many people had thought that the aromatic groups of the ligands the receptors must have been interacting, but this doesn't seem to be the case. There also don't seem to be any interactions between the positively charged parts of the ligands and anionic residues on nearby loops of the protein (which is a rationale I remember from my days in the muscarinic field).

The simulations suggest that the two sites are very much in communication with each other. The width and conformation of the extracellular vestibule space can change according to what allosteric ligand occupies it, and this affects whether the effect on regular ligand binding is positive or negative, and to what degree. There can also, in some cases, be direct electrostatic interactions between the two ligands, for the larger allosteric compounds. I was very glad to see that the Shaw group's simulations suggested some experiments: one set with modified ligands, which would be predicted to affect the