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

Derek Lowe The 2002 Model

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

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

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March 24, 2014

Google's Big Data Flu Flop

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Posted by Derek

Some of you may remember the "Google Flu" effort, where the company was going to try to track outbreaks of influenza in the US by mining Google queries. There was never much clarification about what terms, exactly, they were going to flag as being indicative of someone coming down with the flu, but the hype (or hope) at the time was pretty strong:

Because the relative frequency of certain queries is highly correlated with the percentage of physician visits in which a patient presents with influenza-like symptoms, we can accurately estimate the current level of weekly influenza activity in each region of the United States, with a reporting lag of about one day. . .

So how'd that work out? Not so well. Despite a 2011 paper that seemed to suggest things were going well, the 2013 epidemic wrong-footed the Google Flu Trends (GFT) algorithms pretty thoroughly.

This article in Science finds that the real-world predictive power has been pretty unimpressive. And the reasons behind this failure are not hard to understand, nor were they hard to predict. Anyone who's ever worked with clinical trial data will see this one coming:

The initial version of GFT was a particularly problematic marriage of big and small data. Essentially, the methodology was to find the best matches among 50 million search terms to fit 1152 data points. The odds of finding search terms that match the propensity of the flu but are structurally unrelated, and so do not predict the future, were quite high. GFT developers, in fact, report weeding out seasonal search terms unrelated to the flu but strongly correlated to the CDC data, such as those regarding high school basketball. This should have been a warning that the big data were overfitting the small number of cases—a standard concern in data analysis. This ad hoc method of throwing out peculiar search terms failed when GFT completely missed the nonseasonal 2009 influenza A–H1N1 pandemic.

The Science authors have a larger point to make as well:

“Big data hubris” is the often implicit assumption that big data are a substitute for, rather than a supplement to, traditional data collection and analysis. Elsewhere, we have asserted that there are enormous scientific possibilities in big data. However, quantity of data does not mean that one can ignore foundational issues of measurement and construct validity and reliability and dependencies among data. The core challenge is that most big data that have received popular attention are not the output of instruments designed to produce valid and reliable data amenable for scientific analysis.

The quality of the data matters very, very, much, and quantity is no substitute. You can make a very large and complex structure out of toothpicks and scraps of wood, because those units are well-defined and solid. You cannot do the same with a pile of cotton balls and dryer lint, not even if you have an entire warehouse full of the stuff. If the individual data points are squishy, adding more of them will not fix your analysis problem; it will make it worse.

Since 2011, GFT has missed (almost invariably on the high side) for 108 out of 111 weeks. As the authors show, even low-tech extrapolation from three-week-lagging CDC data would have done a better job. But then, the CDC data are a lot closer to being real numbers. Something to think about next time someone's trying to sell you on a BIg Data project. Only trust the big data when the little data are trustworthy in turn.

Update: a glass-half-full response in the comments.

Comments (18) + TrackBacks (0) | Category: Biological News | Clinical Trials | Infectious Diseases

March 18, 2014

Another DNA-Barcoded Program From GSK

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Posted by Derek

Two more papers have emerged from GSK using their DNA-encoded library platform. I'm always interested to see how this might be working out. One paper is on compounds for the tuberculosis target InhA, and the other is aimed at a lymphocyte protein-protein target, LFA-1. (I've written about this sort of thing previously here, here, and here).

Both of these have some interesting points - I'll cover the LFA-1 work in another post, though. InhA, for its part, is the target of the well-known tuberculosis drug isoniazid, and it has had (as you'd imagine) a good amount of attention over the years, especially since it's not the cleanest drug in the world (although it sure beats having tuberculosis). It's known to be a prodrug for the real active species, and there are also some nasty resistant strains out there, so there's certainly room for something better.
InhA.png
In this case, the GSK group apparently screened several of their DNA-encoded libraries against the target, but the paper only details what happened with one of them, the aminoproline scaffold shown. That would seem to be a pretty reasonable core, but it was one of 22 diamino acids in the library. R1 was 855 different reactants (amide formation, reductive amination, sulfonamides, ureas), and R2 was 857 of the same sorts of things, giving you, theoretically, a library of over 16 million compounds. (If you totaled up the number across the other DNA-encoded libraries, I wonder how many compounds this target saw in total?) Synthesizing a series of hits from this group off the DNA bar codes seems to have worked well, with one compound hitting in the tens of nanomolar range. (The success rate of this step is one of the things that those of us who haven't tried this technique are very interested in hearing about).
InhA2.png
They even pulled out an InhA crystal structure with the compound shown, which really makes this one sound like a poster-child example of the whole technique (and might well be why we're reading about it in J. Med. Chem.) The main thing not to like about the structure is that it has three amides in it, but this is why one runs PK experiments, to see if having three amides is going to be a problem or not. A look at metabolic stability showed that it probably wasn't a bad starting point. Modifying those three regions gave them a glycine methyl ester at P1, which had better potency in both enzyme and cell assays. When you read through the paper, though, it appears that the team eventually had cause to regret having pursued it. A methyl ester is always under suspicion, and in this case it was justified: it wasn't stable under real-world conditions, and every attempt to modify it led to unacceptable losses in activity. It looks like they spent quite a bit of time trying to hang on to it, only to have to give up on it anyway.

In the end, the aminoproline in the middle was still intact (messing with it turned out to be a bad idea). The benzofuran was still there (nothing else was better). The pyrazole had extended from an N-methyl to an N-ethyl (nothing else was better there, either), and the P1 group was now a plain primary amide. A lot of med-chem programs work out like that - you go all around the barn and through the woods, emerging covered with mud and thorns only to find your best compound about fifteen feet away from where you started.

That compound, 65 in the paper, showed clean preliminary tox, along with good PK, potency, and selectivity. In vitro against the bacteria, it worked about as well as the fluoroquinolone moxifloxacin, which is a good level to hit. Unfortunately, when it was tried out in an actual mouse TB infection model, it did basically nothing at all. This, no doubt, is another reason that we're reading about this in J. Med. Chem.. When you read a paper from an industrial group in that journal, you're either visiting a museum or a mausoleum.

That final assay must have been a nasty moment for everyone, and you get the impression that there's still not an explanation for this major disconnect. It's hard to say if they saw it coming - had other compounds been in before, or did the team just save this assay for last and cross their fingers? But either way, the result isn't the fault of the DNA-encoded assay that provided the starting series - that, in this case, seems to have worked exactly as it was supposed to, and up to the infectious animal model study, everything looked pretty good.

Comments (24) + TrackBacks (0) | Category: Chemical Biology | Drug Assays | Infectious Diseases

March 10, 2014

Repurposing for Cervical Cancer

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Posted by Derek

One of the questions I was asked after my talk at Illinois was about repurposing drugs. I replied that there might be some opportunities there, but I didn't think that there were many big ones that had been missed, unless new biology/target ID turned up. Well, here's a news story that contradicts that view of mine, and I'm welcome to be wrong this time.

Researchers in Manchester have been working on the use of lopinavir (an existing drug for HIV) as a therapy for HPV, the cause of most cervical cancers. There's a vaccine for it now, but that doesn't do much for women who are already diagnosed with probable or confirmed disease. But lopinavir therapy seems to do good, and plenty of it. A preliminary trial in Kenya has apparently shown a very high response rate, and they're now raising money for a larger (up to 1,000 patient) trial. I hope that it works out as it appears to - with any luck, HPV-driven disease will gradually disappear from the world in the coming decades, but there will be plenty of patients in the meantime.

As that Daily Telegraph article shows, it wasn't easy getting this work going, because of availability of the drug in the right formulation. Congratulations to the Manchester group and their collaborators in Kenya for being so persistent.

Comments (6) + TrackBacks (0) | Category: Cancer | Clinical Trials | Infectious Diseases

January 28, 2014

Antivirals: "I Love the Deviousness of It All"

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Posted by Derek

Here's a look at some very interesting research on HIV (and a repurposed compound) that I was unable to comment on here. As for the first line of that post, well, I doubt it, but I like to think of myself as rich in spirit. Or something.

Comments (11) + TrackBacks (0) | Category: Biological News | Infectious Diseases

December 12, 2013

Tiny Details, Not So Tiny

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Posted by Derek

Chemjobber has a good post on a set of papers from Pfizer's process chemists. They're preparing filibuvir, and a key step along the way is a Dieckmann cyclization. Well, no problem, say the folks who've never run one of these things - just hit the diester compound with some base, right?

But which base? The example in CJ's post is a good one to show how much variation you can get in these things. As it turned out, LiHMDS was the base of choice, much better than NaHMDS or KHMDS. Potassium t-butoxide was just awful. But the hexamethyldisilazide was even much better than LDA, and those two are normally pretty close. But there were even finer distinctions to be made: it turned out that the reaction was (reproducibly) slightly better or slightly worse with LiHMDS from different suppliers. The difference came down to two processes used to prepare the reagent - via n-BuLi or via lithium metal, and the Pfizer team still isn't sure what the difference is that's making all the difference (see the link for more details).

That's pure, 100-proof process chemistry for you, chasing down these details. It's a good thing for people who don't do that kind of work at all, though, to read some of these papers, because it'll give you an appreciation of variables that otherwise you might not think of at all. When you get down to it, a lot of our reactions are balancing on some fairly wobbly tightropes strung across the energy-surface landscape, and it doesn't take much of a push to send them sliding off in different directions. Choice of cation, of Lewis acid, of solvent, of temperature, order of addition - these and other factors can be thermodynamic and kinetic game-changers. We really don't know too many details about what happens in our reaction flasks.

And a brief med-chem note, for context: filibuvir, into which all this work was put, was dropped from development earlier this year. Sometimes you have to do all the work just to get to the point where you can drop these things - that's the business.

Comments (8) + TrackBacks (0) | Category: Chemical News | Infectious Diseases

December 4, 2013

More Vaccine Fearmongering

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Posted by Derek

Seth Mnookin's The Panic Virus is an excellent overview of the vaccine/autism arguments that raged for many years (and rage still in the heads of the ignorant - sorry, it's gotten to the point where there's no reason to spare anyone's feelings about this issue). Now in this post at PLOS Blogs, he's alerting people to another round of the same stuff, this time about the HPV vaccine:

Over a period of about a month, (Katie Couric's) producer and I spoke for a period of several hours before she told me that the show was no longer interesting in hearing from me on air. Still, I came away from the interaction somewhat heartened: The producer seemed to have a true grasp of the dangers of declining vaccination rates and she stressed repeatedly that her co-workers, including Couric herself, did not view this as an “on the one hand, on the other hand” issue but one in which facts and evidence clearly lined up on one side — the side that overwhelmingly supports the importance and efficacy of vaccines.

Apparently, that was all a load of crap.

Read on for more. One piece of anecdotal data trumps hundreds of thousands of patients worth of actual data, you know. Especially if it's sad. Especially if it gets ratings.

Comments (57) + TrackBacks (0) | Category: Autism | Infectious Diseases | Snake Oil

November 12, 2013

Leaving Antibiotics: An Interview

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Posted by Derek

Here's the (edited) transcript of an interview that Pfizer's VP of clinical research, Charles Knirsch, gave to PBS's Frontline program. The subject was the rise of resistant bacteria - which is a therapeutic area that Pfizer is no longer active in.

And that's the subject of the interview, or one of its main subjects. I get the impression that the interviewer would very much like to tell a story about how big companies walked away to let people die because they couldn't make enough money off of them:

. . .If you look at the course of a therapeutic to treat pneumonia, OK, … we make something, a macrolide, that does that. It’s now generic, and probably the whole course of therapy could cost $30 or $35. Even when it was a branded antibiotic, it may have been a little bit more than that.

So to cure pneumonia, which in some patient populations, particularly the elderly, has a high mortality, that’s what people are willing to pay for a therapeutic. I think that there are differences across different therapeutic areas, but for some reason, with antibacterials in particular, I think that society doesn’t realize the true value.

And did it become incumbent upon you at some point to make choices about which things would be in your portfolio based on this?

Based on our scientific capabilities and the prudent allocation of capital, we do make these choices across the whole portfolio, not just with antibacterials.

But talk to me about the decision that went into antibacterials. Pfizer made a decision in 2011 and announced the decision. Obviously you were making choices among priorities. You had to answer to your shareholders, as you’ve explained, and you shifted. What went into that decision?

I think that clearly our vaccine platforms are state of the art. Our leadership of the vaccine group are some of the best people in the industry or even across the industry or anywhere really. We believe that we have a higher degree of success in those candidates and programs that we are currently prosecuting.

So it’s a portfolio management decision, and if our vaccine for Clostridium difficile —

A bacteria.

Yeah, a bacteria which is a major cause of both morbidity and mortality of patients in hospitals, the type of thing that I would have been consulted on as an infectious disease physician, that in fact we will prevent that, and we’ll have a huge impact on human health in the hospitals.

But did that mean that you had to close down the antibiotic thing to focus on vaccines? Why couldn’t you do both?

Oh, good question. And it’s not a matter of closing down antibiotics. We were having limited success. We had had antibiotics that we would get pretty far along, and a toxicity would emerge either before we even went into human testing or actually in human testing that would lead to discontinuation of those programs. . .

It's that last part that I think is insufficiently appreciated. Several large companies have left the antibiotic field over the years, but several stayed (GlaxoSmithKline and AstraZeneca come to mind). But the ones who stayed were not exactly rewarded for their efforts. Antibacterial drug discovery, even if you pour a lot of money and effort into it, is very painful. And if you're hoping to introduce a mechanism of action into the field, good luck. It's not impossible, but if it were easy to do, more small companies would have rushed in to do it.

Knirsch doesn't have an enviable task here, because the interviewer pushes him pretty hard. Falling back on the phrase "portfolio management decisions" doesn't help much, though:

In our discussion today, I get the sense that you have to make some very ruthless decisions about where to put the company’s capital, about where to invest, about where to put your emphasis. And there are whole areas where you don’t invest, and I guess the question we’re asking is, do you learn lessons about that? When you pulled out of Gram-negative research like that and shifted to vaccines, do you look back on that and say, “We learned something about this”?

These are not ruthless decisions. These are portfolio decisions about how we can serve medical need in the best way. …We want to stay in the business of providing new therapeutics for the future. Our investors require that of us, I think society wants a Pfizer to be doing what we do in 20 years. We make portfolio management decisions.

But you didn’t stay in this field, right? In Gram negatives you didn’t really stay in that field. You told me you shifted to a new approach.

We were not having scientific success, there was no clear regulatory pathway forward, and the return on any innovation did not appear to be something that would support that program going forward.

Introducing the word "ruthless" was a foul, and I'm glad the whistle was blown. I might have been tempted to ask the interviewer what it meant, ruthless, and see where that discussion went. But someone who gives in to temptations like that probably won't make VP at Pfizer.

Comments (51) + TrackBacks (0) | Category: Drug Development | Drug Industry History | Infectious Diseases

October 16, 2013

Holding Back Experimental Details, With Reason

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Posted by Derek

There's a lot of worry these days about the reproducibility of scientific papers (a topic that's come up here many times). And there's reason to believe that the sharing of data, protocols, and materials is not going so well, either.

. . . authors seem less willing to share these additional details about their study protocols than they have been in the past, according to a survey of 389 authors who published studies in the Annals of Internal Medicine. The findings, presented on 9 September at the International Congress on Peer Review and Biomedical Publication in Chicago, found that over the five years studied the percentage saying they would be willing to do so has dropped from almost 80% to only 60%.

A lack of incentives for sharing might be partly to blame. “There's no recognition, no promotion and no profit for scientists who share more information,” says Steven Goodman, a clinical research expert at Stanford University School of Medicine in California, who was part of the team that evaluated the survey results.

But there are two new papers out that deliberately does not share all the details, and it's not hard to see why. This NPR report has the background, but the abstract from the first paper will be enough for anyone in the field:

Clostridium botulinum strain IBCA10-7060, isolated from a patient with infant botulism, produced botulinum neurotoxin type B (BoNT/B) and another BoNT that, by use of the standard mouse bioassay, could not be neutralized by any of the Centers for Disease Control and Prevention–provided monovalent polyclonal botulinum antitoxins raised against BoNT types A–G.

That's not good. Until an antitoxin is available, the sequence of this new neurotoxin will not be published, although the fact of its existence is certainly worth knowing. The Journal of Infectious Diseases has two editorial articles on the issues that this work raises:

(The) identification of a novel, eighth botulinum neurotoxin (BoNT) from a patient with botulism expands our understanding of Clostridium botulinum and BoNT diversity, C. botulinum evolution, and the pathogenesis of botulism, but it also reveals a significant public health vulnerability. This new toxin, BoNT/H, cannot be neutralized by any of the currently available antibotulinum antisera, which means that we have no effective treatment for this form of botulism. Until anti-BoNT/H antitoxin can be created, shown to be effective, and deployed, both the strain itself and the sequence of this toxin (with which recombinant protein can be easily made) pose serious risks to public health because of the unusually severe, widespread harm that could result from misuse of either [3]. Thus, the dilemma faced by these authors, and by society, revolves around the question, should all of the information from this and similar studies be fully disseminated, motivated by the desire to realize all possible benefits from the discovery, or should dissemination of some or all of the information be restricted, with the goal of diminishing the probability of misuse?

I think they've made the right call here. (Last year's disputes about publishing work on a new strain of influenza are in just the same category.) Those studying botulin toxins need to know about this discovery, but given the molecular biology tools available to people, publishing the sequence (or making samples of the organism available) would be asking for potentially major trouble. This, unfortunately, seems to me to be an accurate reading of the world that we find ourselves in. There is a point where the value of having the knowledge out there is outweighed by the danger of. . .having the knowledge out there. This is going to be a case-by-case thing, but we should all be ready for some things to land on this side of the line.

Comments (14) + TrackBacks (0) | Category: Infectious Diseases | The Dark Side | The Scientific Literature

August 16, 2013

An HIV Structure Breakthrough? Or "Complete Rubbish"?

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Posted by Derek

Structural biology needs no introduction for people doing drug discovery. This wasn't always so. Drugs were discovered back in the days when people used to argue about whether those "receptor" thingies were real objects (as opposed to useful conceptual shorthand), and before anyone had any idea of what an enzyme's active site might look like. And even today, there are targets, and whole classes of targets, for which we can't get enough structural information to help us out much.

But when you can get it, structure can be a wonderful thing. X-ray crystallography of proteins, and protein-ligand complexes has revealed so much useful information that it's hard to know where to start. It's not the magic wand - you can't look at an empty binding site and just design something right at your desk that'll be a potent ligand right off the bat. And you can't look at a series of ligand-bound structures and say which one is the most potent, not in most situations, anyway. But you still learn things from X-ray structures that you could never have known otherwise.

It's not the only game in town, either. NMR structures are very useful, although the X-ray ones can be easier to get, especially in these days of automated synchroton beamlines and powerful number-crunching. But what if your protein doesn't crystallize? And what if there are things happening in solution that you'd never pick up on from the crystallized form? You're not going to watch your protein rearrange into a new ligand-bound conformation with X-ray crystallography, that's for sure. No, even though NMR structures can be a pain to get, and have to be carefully interpreted, they'll also show you things you'd never had seen.

And there are more exotic methods. Earlier this summer, there was a startling report of a structure of the HIV surface proteins gp120 and gp41 obtained through cryogenic electron microscopy. This is a very important and very challenging field to work in. What you've got there is a membrane-bound protein-protein interaction, which is just the sort of thing that the other major structure-determination techniques can't handle well. At the same time, though, the number of important proteins involved in this sort of thing is almost beyond listing. Cryo-EM, since it observes the native proteins in their natural environment, without tags or stains, has a lot of potential, but it's been extremely hard to get the sort of resolution with it that's needed on such targets.

Joseph Sodroski's group at Harvard, longtime workers in this area, published their 6-angstrom-resolution structure of the protein complex in PNAS. But according to this new article in Science, the work has been an absolute lightning rod ever since it appeared. Many other structural biologists think that the paper is so flawed that it never should have seen print. No, I'm not exaggerating:

Several respected HIV/AIDS researchers are wowed by the work. But others—structural biologists in particular—assert that the paper is too good to be true and is more likely fantasy than fantastic. "That paper is complete rubbish," charges Richard Henderson, an electron microscopy pioneer at the MRC Laboratory of Molecular Biology in Cambridge, U.K. "It has no redeeming features whatsoever."

. . .Most of the structural biologists and HIV/AIDS researchers Science spoke with, including several reviewers, did not want to speak on the record because of their close relations with Sodroski or fear that they'd be seen as competitors griping—and some indeed are competitors. Two main criticisms emerged. Structural biologists are convinced that Sodroski's group, for technical reasons, could not have obtained a 6-Å resolution structure with the type of microscope they used. The second concern is even more disturbing: They solved the structure of a phantom molecule, not the trimer.

Cryo-EM is an art form. You have to freeze your samples in an aqueous system, but without making ice. The crystals of normal ice formation will do unsightly things to biological samples, on both the macro and micro levels, so you have to form "vitreous ice", a glassy amorphous form of frozen water, which is odd enough that until the 1980s many people considered it impossible. Once you've got your protein particles in this matrix, though, you can't just blast away at full power with your electron beam, because that will also tear things up. You have to take a huge number of runs at lower power, and analyze them through statistical techniques. The Sodolski HIV structure, for example, is the product of 670,000 single-particle images.

But its critics say that it's also the product of wishful thinking.:

The essential problem, they contend, is that Sodroski and Mao "aligned" their trimers to lower-resolution images published before, aiming to refine what was known. This is a popular cryo-EM technique but requires convincing evidence that the particles are there in the first place and rigorous tests to ensure that any improvements are real and not the result of simply finding a spurious agreement with random noise. "They should have done lots of controls that they didn't do," (Sriram) Subramaniam asserts. In an oft-cited experiment that aligns 1000 computer-generated images of white noise to a picture of Albert Einstein sticking out his tongue, the resulting image still clearly shows the famous physicist. "You get a beautiful picture of Albert Einstein out of nothing," Henderson says. "That's exactly what Sodroski and Mao have done. They've taken a previously published structure and put atoms in and gone down into a hole." Sodroski and Mao declined to address specific criticisms about their studies.

Well, they decline to answer them in response to a news item in Science. They've indicated a willingness to take on all comers in the peer-reviewed literature, but otherwise, in print, they're doing the we-stand-by-our-results-no-comment thing. Sodroski himself, with his level of experience in the field, seems ready to defend this paper vigorously, but there seem to be plenty of others willing to attack. We'll have to see how this plays out in the coming months - I'll update as things develop.

Comments (34) + TrackBacks (0) | Category: Analytical Chemistry | Biological News | In Silico | Infectious Diseases

July 24, 2013

Stuart Schreiber at the Challenges in Chemical Biology Conference

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Posted by Derek

I'm listening to Stuart Schreiber make his case for diversity-oriented synthesis (DOS) as a way to interrogate biochemistry. I've written about this idea a number of times here, but I'm always glad to hear the pitch right from the source.

Schreiber's team has about 100,000 compounds from DOS now, all of which are searchable at PubChem. He says that they have about 15mg of each of them in the archives, which is a pretty solid collection. They've been trying to maximize the biochemical diversity of their screening (see here and here for examples), and they're also (as noted here) building up a collection of fragments, which he says will be used for high-concentration screening.

He's also updating some efforts with the Gates Foundation to do cell-based antimalarial screening with the DOS compounds. They have 468 compounds that they're now concentrating on, and checking these against resistant strains indicates that some of them may well be working through unusual mechanisms (others, of course, are apparently hitting the known ones). He's showing structures, and they are very DOSsy indeed - macrocycles, spiro rings, chirality all over. But since these assay are done in cells, some large hoops have already been jumped through.

He's also talking about the Broad Institutes efforts to profile small-molecule behavior in numerous tumor cell lines. Here's a new public portal site on this, and there's apparently a paper accepted at Cell on it as well. They have hundreds of cell lines, from all sorts of sources, and are testing those against an "informer set" of small-molecule probes and known drugs. They're trying to make this a collection of very selective compounds, targeting a wide variety of different targets throughout the cell. There are kinase inhibitors, epigenetic compounds, and a long list of known oncology candidates, as well as many other compounds that don't hit obvious cancer targets.

They're finding out a lot of interesting things about target ID with this set. Schreiber says that this work has made him more interested in gene expression profiles than in mutations per se. Here, he says, is an example of what he's talking about. Another example is the recent report of the natural product austocystin, which seems to be activated by CYP metabolism. The Broad platform has identified CYP2J2 as the likely candidate.

There's an awful lot of work on these slides (and an awful lot of funding is apparent, too). I think that the "Cancer Therapeutics Response Portal" mentioned above is well worth checking out - I'll be rooting through it after the meeting.

Comments (23) + TrackBacks (0) | Category: Cancer | Chemical Biology | Infectious Diseases

June 14, 2013

One. . .Million. . .Pounds (For a New Antibiotic?)

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Posted by Derek

Via Stuart Cantrill on Twitter, I see that UK Prime Minister David Cameron is prepared to announce a prize for anyone who can "identify and solve the biggest problem of our time". He's leaving that open, and his examples are apparently ". . .the next penicillin, aeroplane or world wide web".

I like the idea of prizes for research and invention. The thing is, the person who invents the next airplane or World Wide Web will probably do pretty well off it through the normal mechanisms. And it's worth thinking about the very, very different pathways these three inventions took, both in their discovery and their development. While thinking about that, keep in mind the difference between those two.

The Wright's first powered airplane, a huge step in human technology, was good for carrying one person (lying prone) for a few hundred yards in a good wind. Tim Berners-Lee's first Web page, another huge step, was a brief bit of code on one server at CERN, and mostly told people about itself. Penicillin, in its early days, was famously so rare that the urine of the earliest patients was collected and extracted in order not to waste any of the excreted drug. And even that was a long way from Fleming's keen-eyed discovery of the mold's antibacterial activity. A more vivid example than penicillin of the need for huge amounts of development from an early discovery is hard to find.

And how does one assign credit to the winner? Many (most) of these discoveries take a lot of people to realize them - certainly, by the time it's clear that they're great discoveries. Alexander Fleming (very properly) gets a lot of credit for the initial discovery of penicillin, but if the world had depended on him for its supply, it would have been very much out of luck. He had a very hard time getting anything going for nearly ten years after the initial discovery, and not for lack of trying. The phrase "Without Fleming, no Chain; without Chain, no Florey; without Florey, no Heatley; without Heatley, no penicillin" properly assigns credit to a lot of scientists that most people have never heard of.

Those are all points worth thinking about, if you're thinking about Cameron's prize, or if you're David Cameron. But that's not all. Here's the real kicker: he's offering one million pounds for it ($1.56 million as of this morning). This is delusional. The number of great discoveries that can be achieved for that sort of money is, I hate to say, rather small these days. A theoretical result in math or physics might certainly be accomplished in that range, but reducing it to practice is something else entirely. I can speak to the "next penicillin" part of the example, and I can say (without fear of contradiction from anyone who knows the tiniest bit about the subject) that a million pounds could not, under any circumstances, tell you if you had the next penicillin. That's off by a factor of a hundred, if you just want to take something as far as a solid start.

There's another problem with this amount: in general, anything that's worth that much is actually worth a lot more; there's no such thing as a great, world-altering discovery that's worth only a million pounds. I fear that this will be an ornament around the neck of whoever wins it, and little more. If Cameron's committee wants to really offer a prize in line with the worth of such a discovery, they should crank things up to a few hundred million pounds - at least - and see what happens. As it stands, the current idea is like me offering a twenty-dollar bill to anyone who brings me a bar of gold.

Comments (28) + TrackBacks (0) | Category: Current Events | Drug Industry History | Infectious Diseases | Who Discovers and Why

May 29, 2013

Sulfa Side Effects, Decades Later

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Posted by Derek

You'd think that by now we'd know all there is to know about the side effects of sulfa drugs, wouldn't you? These were the top-flight antibiotics about 80 years ago, remember, and they've been in use (in one form or another) ever since. But some people have had pronounced CNS side effects from their use, and it's never been clear why.

Until now, that is. Here's a new paper in Science that shows that this class of drugs inhibits the synthesis of tetrahydrobiopterin, an essential cofactor for a number of hydroxylase and reductase enzymes. And that in turn interferes with neurotransmitter levels, specifically dopamine and serotonin. The specific culprit here seems to be sepiapterin reductase (SPR). Here's a summary at C&E News.

This just goes to show you how much there is to know, even about things that have been around forever (by drug industry standards). And every time something like this comes up, I wonder what else there is that we haven't uncovered yet. . .

Comments (17) + TrackBacks (0) | Category: Infectious Diseases | Toxicology

May 17, 2013

A Little Ranbaxy Example

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Posted by Derek

Compare and contrast. Here we have Krishnan Ramalingam, from Ranbaxy's Corporate Communications department, in 2006:

Being a global pharmaceutical major, Ranbaxy took a deliberate decision to pool its resources to fight neglected disease segments. . .Ranbaxy strongly felt that generic antiretrovirals are essential in fighting the world-wide struggle against HIV/AIDS, and therefore took a conscious decision to embark upon providing high quality affordable generics for patients around the world, specifically for the benefit of Least Developed Countries. . .Since 2001, Ranbaxy has been providing antiretroviral medicines of high quality at affordable prices for HIV/AIDS affected countries for patients who might not otherwise be able to gain access to this therapy.

And here we have them in an advertorial section of the South African Mail and Guardian newspaper, earlier this year:

Ranbaxy has a long standing relationship with Africa. It was the first Indian pharmaceutical company to set up a manufacturing facility in Nigeria, in the late 1970s. Since then, the company has established a strong presence in 44 of the 54 African countries with the aim of providing quality medicines and improving access. . .Ranbaxy is a prominent supplier of Antiretroviral (ARV) products in South Africa through its subsidiary Sonke Pharmaceuticals. It is the second largest supplier of high quality affordable ARV products in South Africa which are also extensively used in government programs providing access to ARV medicine to millions.

Yes, as Ranbaxy says on its own web site: "At Ranbaxy, we believe that Anti-retroviral (ARV) therapy is an essential tool in waging the war against HIV/AIDS. . .We estimate currently close to a million patients worldwide use our ARV products for their daily treatment needs. We have been associated with this cause since 2001 and were among the first generic companies to offer ARVs to various National AIDS treatment programmes in Africa. We were also responsible for making these drugs affordable in order to improve access. . ."

And now we descend from the heights. Here, in a vivid example of revealed preference versus stated preference, is what was really going on, from that Fortune article I linked to yesterday:

. . .as the company prepared to resubmit its ARV data to WHO, the company's HIV project manager reiterated the point of the company's new strategy in an e-mail, cc'ed to CEO Tempest. "We have been reasonably successful in keeping WHO from looking closely at the stability data in the past," the manager wrote, adding, "The last thing we want is to have another inspection at Dewas until we fix all the process and validation issues once and for all."

. . .(Dinesh) Thakur knew the drugs weren't good. They had high impurities, degraded easily, and would be useless at best in hot, humid conditions. They would be taken by the world's poorest patients in sub-Saharan Africa, who had almost no medical infrastructure and no recourse for complaints. The injustice made him livid.

Ranbaxy executives didn't care, says Kathy Spreen, and made little effort to conceal it. In a conference call with a dozen company executives, one brushed aside her fears about the quality of the AIDS medicine Ranbaxy was supplying for Africa. "Who cares?" he said, according to Spreen. "It's just blacks dying."

I have said many vituperative things about HIV hucksters like Matthias Rath, who have told patient in South Africa to throw away their antiviral medications and take his vitamin supplements instead. What, then, can I say about people like this, who callously and intentionally provided junk, labeled as what were supposed to be effective drugs, to people with no other choice and no recourse? If this is not criminal conduct, I'd very much like to know what is.

And why is no one going to jail? I'm suggesting jail as a civilized alternative to a barbaric, but more appealingly direct form of justice: shipping the people who did this off to live in a shack somewhere in southern Africa, infected with HIV, and having them subsist as best they can on the drugs that Ranbaxy found fit for their sort.

Comments (43) + TrackBacks (0) | Category: Infectious Diseases | The Dark Side

May 7, 2013

Another Germ Theory Victory - Back Pain?

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Posted by Derek

The "New Germ Theory" people may have notched up another one: a pair of reports out from a team in Denmark strongly suggest that many cases of chronic low back pain are due to low-grade bacterial infection. They've identified causative agents (Propionibacterium acnes) by isolating them from tissue, and showed impressive success in the clinic by treating back pain patients with a lengthy course of antibiotics. Paul Ewald is surely smiling about this news, although (as mentioned here) he has some ideas about the drug industry that I can't endorse.

So first we find out that stomach ulcers are not due to over-dominant mothers, and now this. What other hard-to-diagnose infections are we missing? Update - such as obesity, maybe?

Comments (25) + TrackBacks (0) | Category: Infectious Diseases

March 14, 2013

Does Baldness Get More Funding Than Malaria?

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Posted by Derek

OK, let's fact-check Bill Gates today, shall we?

Capitalism means that there is much more research into male baldness than there is into diseases such as malaria, which mostly affect poor people, said Bill Gates, speaking at the Royal Academy of Engineering's Global Grand Challenges Summit.

"Our priorities are tilted by marketplace imperatives," he said. "The malaria vaccine in humanist terms is the biggest need. But it gets virtually no funding. But if you are working on male baldness or other things you get an order of magnitude more research funding because of the voice in the marketplace than something like malaria."

Gates' larger point, that tropical diseases are an example of market failure, stands. But I don't think this example does. I have never yet worked on any project in industry that had anything to do with baldness, while I have actually touched on malaria. Looking around the scientific literature, I see many more publications on potential malaria drugs than I see potential baldness drugs (in fact, I'm not sure if I've ever seen anything on the latter, after minoxidil - and its hair-growth effects were discovered by accident during a cardiovascular program). Maybe I'm reading the wrong journals.

But then, Gates also seems to buy into the critical-shortage-of-STEM idea:

With regards to encouraging more students into STEM education, Gates said: "It's kind of surprising that we have such a deficit of people going into those fields. Look at where you can have the most interesting job that pays well and will have impact on society -- all three of those things line up to say science and engineering and yet in most rich countries we see decline. Asia is an exception."

The problem is, there aren't as many of these interesting, well-paying jobs around as there used to be. Any discussion of the STEM education issue that doesn't deal with that angle is (to say the least) incomplete.

Comments (28) + TrackBacks (0) | Category: Drug Development | Drug Industry History | Infectious Diseases

February 28, 2013

IBM's Watson Does Drug Discovery?

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Posted by Derek

I saw this story this morning, about IBM looking for more markets for its Watson information-sifting system (the one that performed so publicly on "Jeopardy". And this caught my eye for sure:

John Baldoni, senior vice president for technology and science at GlaxoSmithKline, got in touch with I.B.M. shortly after watching Watson’s “Jeopardy” triumph. He was struck that Watson frequently had the right answer, he said, “but what really impressed me was that it so quickly sifted out so many wrong answers.”

That is a huge challenge in drug discovery, which amounts to making a high-stakes bet, over years of testing, on the success of a chemical compound. The failure rate is high. Improving the odds, Mr. Baldoni said, could have a huge payoff economically and medically.

Glaxo and I.B.M. researchers put Watson through a test run. They fed it all the literature on malaria, known anti-malarial drugs and other chemical compounds. Watson correctly identified known anti-malarial drugs, and suggested 15 other compounds as potential drugs to combat malaria. The two companies are now discussing other projects.

“It doesn’t just answer questions, it encourages you to think more widely,” said Catherine E. Peishoff, vice president for computational and structural chemistry at Glaxo. “It essentially says, ‘Look over here, think about this.’ That’s one of the exciting things about this technology.”

Now, without seeing some structures and naming some names, it's completely impossible to say how valuable the Watson suggestions were. But I would very much like to know on what basis these other compounds were suggested: structural similarity? Mechanisms in common? Mechanisms that are in the same pathway, but hadn't been specifically looked at for malaria? Something else entirely? Unfortunately, we're probably not going to be able to find out, unless GSK is forthcoming with more details.

Eventually, there's coing to be another, somewhat more disturbing answer to that "what basis?" question. As this Slate article says, we could well get to the point where such systems make discoveries or correlations that are correct, but beyond our ability to figure out. Watson is most certainly not there yet. I don't think anything is, or is really all that close. But that doesn't mean it won't happen.

For a look at what this might be like, see Ted Chiang's story "Catching Crumbs From the Table", which appeared first in Nature, and then in his collection Stories of Your Life and Others, which I highly recommend, as "The Evolution of Human Science".

Comments (32) + TrackBacks (0) | Category: In Silico | Infectious Diseases

February 13, 2013

Mouse Models of Inflammation Are Basically Worthless. Now We Know.

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Posted by Derek

We go through a lot of mice in this business. They're generally the first animal that a potential drug runs up against: in almost every case, you dose mice to check pharmacokinetics (blood levels and duration), and many areas have key disease models that run in mice as well. That's because we know a lot about mouse genetics (compared to other animals), and we have a wide range of natural mutants, engineered gene-knockout animals (difficult or impossible to do with most other species), and chimeric strains with all sorts of human proteins substituted back in. I would not wish to hazard a guess as to how many types of mice have been developed in biomedical labs over the years; it is a large number representing a huge amount of effort.

But are mice always telling us the right thing? I've written about this problem before, and it certainly hasn't gone away. The key things to remember about any animal model is that (1) it's a model, and (2) it's in an animal. Not a human. But it can be surprisingly hard to keep these in mind, because there's no other way for a compound to become a drug other than going through the mice, rats, etc. No regulatory agency on Earth (OK, with the possible exception of North Korea) will let a compound through unless it's been through numerous well-controlled animal studies, for short- and long-term toxicity at the very least.

These thoughts are prompted by an interesting and alarming paper that's come out in PNAS: "Genomic responses in mouse models poorly mimic human inflammatory diseases". And that's the take-away right there, which is demonstrated comprehensively and with attention to detail.

Murine models have been extensively used in recent decades to identify and test drug candidates for subsequent human trials. However, few of these human trials have shown success. The success rate is even worse for those trials in the field of inflammation, a condition present in many human diseases. To date, there have been nearly 150 clinical trials testing candidate agents intended to block the inflammatory response in critically ill patients, and every one of these trials failed. Despite commentaries that question the merit of an overreliance of animal systems to model human immunology, in the absence of systematic evidence, investigators and public regulators assume that results from animal research reflect human disease. To date, there have been no studies to systematically evaluate, on a molecular basis, how well the murine clinical models mimic human inflammatory diseases in patients.

What this large multicenter team has found is that while various inflammation stresses (trauma, burns, endotoxins) in humans tend to go through pretty much the same pathways, the same is not true for mice. Not only do they show very different responses from humans (as measured by gene up- and down-regulation, among other things), they show different responses to each sort of stress. Humans and mice differ in what genes are called on, in their timing and duration of expression, and in what general pathways these gene products are found. Mice are completely inappropriate models for any study of human inflammation.

And there are a lot of potential reasons why this turns out to be so:

There are multiple considerations to our finding that transcriptional response in mouse models reflects human diseases so poorly, including the evolutional distance between mice and humans, the complexity of the human disease, the inbred nature of the mouse model, and often, the use of single mechanistic models. In addition, differences in cellular composition between mouse and human tissues can contribute to the differences seen in the molecular response. Additionally, the different temporal spans of recovery from disease between patients and mouse models are an inherent problem in the use of mouse models. Late events related to the clinical care of the patients (such as fluids, drugs, surgery, and life support) likely alter genomic responses that are not captured in murine models.

But even with all the variables inherent in the human data, our inflammation response seems to be remarkably coherent. It's just not what you see in mice. Mice have had different evolutionary pressures over the years than we have; their heterogeneous response to various sorts of stress is what's served them well, for whatever reasons.

There are several very large and ugly questions raised by this work. All of us who do biomedical research know that mice are not humans (nor are rats, nor are dogs, etc.) But, as mentioned above, it's easy to take this as a truism - sure, sure, knew that - because all our paths to human go through mice and the like. The New York Times article on this paper illustrates the sort of habits that you get into (emphasis below added):

The new study, which took 10 years and involved 39 researchers from across the country, began by studying white blood cells from hundreds of patients with severe burns, trauma or sepsis to see what genes are being used by white blood cells when responding to these danger signals.

The researchers found some interesting patterns and accumulated a large, rigorously collected data set that should help move the field forward, said Ronald W. Davis, a genomics expert at Stanford University and a lead author of the new paper. Some patterns seemed to predict who would survive and who would end up in intensive care, clinging to life and, often, dying.

The group had tried to publish its findings in several papers. One objection, Dr. Davis said, was that the researchers had not shown the same gene response had happened in mice.

“They were so used to doing mouse studies that they thought that was how you validate things,” he said. “They are so ingrained in trying to cure mice that they forget we are trying to cure humans.”

“That started us thinking,” he continued. “Is it the same in the mouse or not?”

What's more, the article says that this paper was rejected from Science and Nature, among other venues. And one of the lead authors says that the reviewers mostly seemed to be saying that the paper had to be wrong. They weren't sure where things had gone wrong, but a paper saying that murine models were just totally inappropriate had to be wrong somehow.

We need to stop being afraid of the obvious, if we can. "Mice aren't humans" is about as obvious a statement as you can get, but the limitations of animal models are taken so much for granted that we actually dislike being told that they're even worse than we thought. We aren't trying to cure mice. We aren't trying to make perfect diseases models and beautiful screening cascades. We aren't trying to perfectly match molecular targets with diseases, and targets with compounds. Not all the time, we aren't. We're trying to find therapies that work, and that goal doesn't always line up with those others. As painful as it is to admit.

Comments (50) + TrackBacks (0) | Category: Animal Testing | Biological News | Drug Assays | Infectious Diseases

January 24, 2013

Three Rings in a Row

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Posted by Derek

GRL.png
Here's a structure that caught me eye, in this paper from Georgia State and Purdue. That's a nice-looking group stuck on the side of their HIV protease inhibitor; I don't think I've ever seen three fused THF rings before, and if I have, it certainly wasn't in a drug candidate. From the X-ray structure, it seems to be making some beneficial interactions out in the P2 site.

This is an analog these are analogs of darunavir, which has two THFs fused in similar fashion. That compound's behavior in vivo is well worked out - most of the metabolism is cleavage of the carbamate. Both with and without that, there's a bunch of scattered hydroxylation and glucuronidation; the bis-THF survives just fine. (That's worth thinking about. Most of us would be suspicious of that group, but it's pretty robust in this case). I'd be interested in seeing if this new structure behaves similarly, or if it's now more sensitive to gastric fluid and the like. No data of that sort is presented in this paper (it's an academic group, after all), but perhaps we'll find out eventually.

Comments (5) + TrackBacks (0) | Category: Infectious Diseases

January 15, 2013

Is Obesity An Infectious Disease?

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Posted by Derek

Like many people, I have a weakness for "We've had it all wrong!" explanations. Here's another one, or part of one: is obesity an infectious disease?

During our clinical studies, we found that Enterobacter, a genus of opportunistic, endotoxin-producing pathogens, made up 35% of the gut bacteria in a morbidly obese volunteer (weight 174.8 kg, body mass index 58.8 kg m−2) suffering from diabetes, hypertension and other serious metabolic deteriorations. . .

. . .After 9 weeks on (a special diet), this Enterobacter population in the volunteer's gut reduced to 1.8%, and became undetectable by the end of the 23-week trial, as shown in the clone library analysis. The serum–endotoxin load, measured as LPS-binding protein, dropped markedly during weight loss, along with substantial improvement of inflammation, decreased level of interleukin-6 and increased adiponectin. Metagenomic sequencing of the volunteer's fecal samples at 0, 9 and 23 weeks on the WTP diet confirmed that during weight loss, the Enterobacteriaceae family was the most significantly reduced population. . .

They went on to do the full Koch workup, by taking an isolated Enterobacter strain from the human patient and introducing it into gnotobiotic (germ-free) mice. These mice are usually somewhat resistant to becoming obese on a high-fat diet, but after being inoculated with the bacterial sample, they put on substantial weight, became insulin resistant, and showed numerous (consistent) alterations in their lipid and glucose handling pathways. Interestingly, the germ-free mice that were inoculated with bacteria and fed normal chow did not show these effects.

The hypothesis is that the endotoxin-producing bacteria are causing a low-grade chronic inflammation in the gut, which is exacerbated to a more systemic form by the handling of excess lipids and fatty acids. The endotoxin itself may be swept up in the chylomicrons and translocated through the gut wall. The summary:

. . .This work suggests that the overgrowth of an endotoxin-producing gut bacterium is a contributing factor to, rather than a consequence of, the metabolic deteriorations in its human host. In fact, this strain B29 is probably not the only contributor to human obesity in vivo, and its relative contribution needs to be assessed. Nevertheless, by following the protocol established in this study, we hope to identify more such obesity-inducing bacteria from various human populations, gain a better understanding of the molecular mechanisms of their interactions with other members of the gut microbiota, diet and host for obesity, and develop new strategies for reducing the devastating epidemic of metabolic diseases.

Considering the bacterial origin of ulcers, I think this is a theory that needs to be taken seriously, and I'm glad to see it getting checked out. We've been hearing a lot the last few years about the interaction between human physiology and our associated bacterial population, but the attention is deserved. The problem is, we're only beginning to understand what these ecosystems are like, how they can be disordered, and what the consequences are. Anyone telling you that they have it figured out at this point is probably trying to sell you something. It's worth the time to figure out, though. . .

Comments (32) + TrackBacks (0) | Category: Biological News | Diabetes and Obesity | Infectious Diseases

October 8, 2012

Nasty Drug Molecules: Amphotericin B

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Posted by Derek

You've probably seen the headlines about fungal meningitis showing up, caused (it appears) by contaminated injectable steroid supplies. As soon as I heard these stories, I wondered what you treat this condition with, and my first thought was "Amphotericin B, most likely". And so it appears.
amphotericin%20jpeg.jpg
That compound still seems to be the usual answer for the nastiest fungal infections, a role it's occupied for decades. That's not by choice. It's an awful compound in many ways, as illustrated by that Wikipedia article linked above:

Amphotericin B is well known for its severe and potentially lethal side-effects. Very often, a serious acute reaction after the infusion (1 to 3 hours later) is noted, consisting of high fever, shaking chills, hypotension, anorexia, nausea, vomiting, headache, dyspnea and tachypnea, drowsiness, and generalized weakness. This reaction sometimes subsides with later applications of the drug, and may in part be due to histamine liberation. An increase in prostaglandin synthesis may also play a role. This nearly universal febrile response necessitates a critical (and diagnostically difficult) professional determination as to whether the onset of high fever is a novel symptom of a fast-progressing disease, or merely the induced effect of the drug.

Organ damage is also distressingly common, and patients who are dying of a systemic fungal infection can suddenly find themselves dying instead of kidney or liver failure. As you'd imagine from that structure, it has to be given intravenously, unless you're treating an oral infection. (Note that it's quite similar to the common topic medicine nystatin). The drug works, as far as anyone can tell, by opening pores in cell membranes, particularly associating with sterols. It seems to have a greater affinity for ergosterol (found in fungi) over cholesterol, which gives it whatever therapeutic window it has.

People have tried for years to replace Amphotericin B, but it remains with us. If you're taking it, you are probably in a bad way.

Comments (22) + TrackBacks (0) | Category: Infectious Diseases

September 4, 2012

A New Malaria Compound

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Posted by Derek

There have been many headlines in recent days about a potential malaria cure. I'm not sure what set these off at this time, since the paper describing the work came out back in the spring, but it's certainly worth a look.

This all came out of the Medicines for Malaria Venture, a nonprofit group that has been working with various industrial and academic groups in many areas of malaria research. This is funded through a wide range of donors (corporations, foundations, international agencies), and work has taken place all over the world. In this case (PDF), things began with a collection of about 36,000 compounds (biased towards kinase inhibitor scaffolds) from BioFocus in the UK. These were screened (high-throughput phenotypic readout) at the Eskitis Institute in Australia, and a series of compounds was identified for structure-activity studies. This phase of the work was a three-way collaboration between a chemistry team at the University of Cape Town (led by Prof. Kelly Chibale), biology assay teams at the Swiss Tropical and Public Health Institute, and pharmacokinetics at the Center for Drug Candidate Optimization at Monash University in Australia.
MMV%20compound%2015.png
An extensive SAR workup on the lead series identified some metabolically labile parts of the molecule over on that left-hand side pyridine. These could fortunately be changed without impairing the efficacy against the malaria parasites. The sulfonyl group seems to be required, as does the aminopyridine. These efforts led to the compound shown, MMV390048, which has good blood levels, passes in vitro safety tests, and is curative in a Plasmodium berghei mouse model at a single dose of 30 mg/kg. That's a very promising compound, from the looks of it, since that's better than the existing antimalarials can do. It's also active against drug-resistant strains, as well it might be (see below). Last month the MMV selected it for clinical development.

So how does this compound work? The medicinal chemists in the audience will have looked at that structure and said "kinase inhibitor", and that has to be where to put your money. That, in fact, appears to have been the entire motivation to screen the BioFocus collection. Kinase targets in Plasmodium have been getting attention for several years now; the parasite has a number of enzymes in this class, and they're different enough from human kinases to make attractive targets. (To that point, I have not been able to find results of this latest compound's profile when run against a panel of human kinases, although you'd think that this has surely been done by now). Importantly, none of the existing antimalarials work through such mechanisms, so the parasites have not had a chance to work up any resistance.

But resistance will come. It always does. The best hope for the kinase-based inhibitors is that they'll hit several malaria enzymes at once, which gives the organisms a bigger evolutionary barrier to jump over. The question is whether you can do that without hitting anything bad in the human kinome, but for the relatively short duration of acute malaria treatment, you should be able to get away with quite a bit. Throwing this compound and the existing antimalarials at the parasites simultaneously will really give them something to occupy themselves.

I'll follow the development of this compound with interest. It's just about to hit the really hard part of drug research - human beings in the clinic. This is where we have our wonderful 90% or so failure rates, although those figures are generally better for anti-infectives, as far as I can tell. Best of luck to everyone involved. I hope it works.

Comments (27) + TrackBacks (0) | Category: Drug Development | Infectious Diseases

May 21, 2012

A New Way to Kill Amoebas, From An Old Drug

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Posted by Derek

Here's a good example of phenotypic screening coming through with something interesting and worthwhile: they screened against Entamoeba histolytica, the protozooan that causes amoebic dysentery and kills tens of thousands of people every year. (Press coverage here).

It wasn't easy. The organism is an anaerobe, which is a bad fit for most robotic equipment, and engineering a decent readout for the assay wasn't straightforward, either. They did have a good positive control, though - the nitroimidazole drug metronidazole, which is the only agent approved currently against the parasite (and to which it's becoming resistant). A screen of nearly a thousand known drugs and bioactive compounds showed eleven hits, of which one (auranofin) was much more active than metronidazole itself.

Auranofin's an old arthritis drug. It's a believable result, because the compound has also been shown to have activity against trypanosomes, Leishmania parasites, and Plasmodium malaria parasites. This broad-spectrum activity makes some sense when you realize that the drug's main function is to serve as a delivery vehicle for elemental gold, whose activity in arthritis is well-documented but largely unexplained. (That activity is also the basis for persistent theories that arthritis may have an infectious-disease component).

The target in this case may well be arsenite-inducible RNA-associated protein (AIRAP), which was strongly induced by drug treatment. The paper notes that arsenite and auranofin are both known inhibitors of thioredoxin reductase, which strongly suggests that this is the mechanistic target here. The organism's anaerobic lifestyle fits in with that; this enzyme would presumably be its main (perhaps only) path for scavenging reactive oxygen species. It has a number of important cysteine residues, which are very plausible candidates for binding to a metal like gold. And sure enough, auranofin (and two analogs) are potent inhibitors of purified form of the amoeba enzyme.

The paper takes the story all the way to animal models, where auranofin completely outperforms metronidazole. The FDA has now given it orphan-drug status for amebiasis, and the way appears clear for a completely new therapeutic option in this disease. Congratulations to all involved; this is excellent work.

Comments (10) + TrackBacks (0) | Category: Academia (vs. Industry) | Drug Assays | Drug Development | Infectious Diseases

A Molecular Craigslist?

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Posted by Derek

Mat Todd at the University of Sydney (whose open-source drug discovery work on schistosomiasis I wrote about here) has an interesting chemical suggestion. His lab is also involved in antimalarial work (here's an update, for those interested, and I hope to post about this effort more specifically). He's wondering about whether there's room for a "Molecular Craigslist" for efforts like these:

Imagine there is a group somewhere with expertise in making these kinds of compounds, and who might want to make some analogs as part of a student project, in return for collaboration and co-authorship? What about a Uni lab which might be interested in making these compounds as part of an undergrad lab course?

Wouldn’t it be good if we could post the structure of a molecule somewhere and have people bid on providing it? i.e. anyone can bid – commercial suppliers, donators, students?

Is there anything like this? Well, databases like Zinc and Pubchem can help in identifying commercial suppliers and papers/patents where groups have made related compounds, but there’s no tendering process where people can post molecules they want. Science Exchange has, I think, commercial suppliers, but not a facility to allow people to donate (I may be wrong), or people to volunteer to make compounds (rather than be listed as generic suppliers. Presumably the same goes for eMolecules, and Molport?

Is there a niche here for a light client that permits the process I’m talking about? Paste your Smiles, post the molecule, specifying a purpose (optional), timeframe, amount, type of analytical data needed, and let the bidding commence?

The closest thing I can think of is Innocentive, which might be pretty close to what he's talking about. It's reasonably chemistry-focused as well. Any thoughts out there?

Comments (19) + TrackBacks (0) | Category: Academia (vs. Industry) | Business and Markets | Drug Development | Infectious Diseases

April 30, 2012

India's First Drug Isn't India's First Drug

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Posted by Derek

There have been a number of headlines the last few days about Ranbaxy's Synriam, an antimalarial that's being touted as the first new drug developed inside the Indian pharma industry (and Ranbaxy as the first Indian company to do it).

But that's not quite true, as this post from The Allotrope makes clear. (Its author, Akshat Rathi, found one of my posts when he started digging into the story). Yes, Synriam is a mixture of a known antimalarial (piperaquine) and arterolane. And arterolane was definitely not discovered in India. It was part of a joint effort from the US, UK, Australia, and Switzerland, coordinated by the Swiss-based Medicines for Malaria Venture.

Ranbaxy did take on the late-stage development of this drug combination, after MMV backed out due to no-so-impressive performance in the clinic. As Rathi puts it:

Although Synriam does not qualify as ‘India’s first new drug’ (because none of its active ingredients were wholly developed in India), Ranbaxy deserves credit for being the first Indian pharmaceutical company to launch an NCE before it was launched anywhere else in the world.

And that's something that not many countries have done. I just wish that Ranbaxy were a little more honest about that in their press release.

Comments (8) + TrackBacks (0) | Category: Drug Development | Infectious Diseases

April 25, 2012

DHFR Inhibitors Revisited: A Word From the Authors (and Reviewers)

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Posted by Derek

The other day, I had some uncomplimentary things to say about a recent J. Med. Chem. paper on fragment-based dihydrofolate reductase inhibitors. Well, I know that I don't say these things into a vacuum, by any means, but in this case the lead author has written me about the work, and a reviewer of the paper has showed up in the comments. So perhaps this is a topic worth revisiting?

First, I'll give Prof. Joelle Pelletier of U. Montreal the floor to make the case for the defense. Links added are mine, for background; I take responsibility for those, and I hope they're helpful.

I was informed of your recent blog entitled ‘How do these things get published’. I am corresponding author of that paper. I would like to bring to your attention a crucial point that was incorrectly presented in your analysis: the target enzyme is not that which you think it is, i.e.: it is not a DHFR that is part of ‘a class of enzymes that's been worked on for decades’.

Indeed, it would make no sense to report weak and heavy inhibitors against ‘regular’ DHFRs (known as ‘type I DHFRs’), considering the number of efficient DHFR inhibitors we already know. But this target has no sequence or structural homology with type I DHFRs. It is a completely different protein that offers an alternate path to production of tetrahydrofolate (see top of second page of the article). It has apparently evolved recently, as a bacterial response to trimethoprim being introduced into the environment since the ‘60’s. Because that protein is evolutionarily unrelated to regular DHFRs, it doesn’t bind trimethoprim and is thus intrinsically trimethoprim resistant; it isn’t inhibited by other inhibitors of regular DHFRs either. There have been no efforts to date to inhibit this drug resistance enzyme, despite its increasing prevalence in clinical and veterinary settings, and in food and wastewater (see first page of article). As a result, we know nothing about how to prevent it from providing drug resistance. Our paper is thus the first foray into inhibiting this new target – one which presents both the beauty and the difficulty of complex symmetry.

Regular (type I) DHFRs are monomeric enzymes with an extended active-site cleft. They are chromosomally-encoded in all living cells where they are essential for cellular proliferation. Our target, type II R67 DHFR, is carried on a plasmid, allowing rapid dissemination between bacterial species. It is an unusual homotetrameric, doughnut-style enzyme with the particularity of having a single active site in the doughnut hole. That’s unusual because multimeric enzymes typically have the same number of active sites as they do monomers. The result is that the active site tunnel, shown in Figure 4 a, has 222 symmetry. Thus, the front and back entrances to the active site tunnel are identical. And that’s why designing long symmetrical molecules makes sense: they have the potential of threading through the tunnel, where the symmetry of the inhibitor would match the symmetry of the target. If they don’t string through but fold up into a ‘U”, it still makes sense: the top and bottom of the tunnel are also alike, again allowing a match-up of symmetry. Please note that this symmetry does create a bit of a crystallographer’s nightmare at the center of the tunnel where the axes of symmetry meet; again, it is an unusual system.

You have referred to our ‘small, poorly documented library of fragment compounds’. As for the poor documentation, the point is that we have very little prior information on the ligands of this new target, other than its substrates. We cast as wide a net as we could within a loosely defined chemical class, using the chemicals we have access to. Unfortunately, I don’t have access to a full fragment library, but am open to collaboration.

As a result of extending the fragments, the ligand efficiency does take a beating… so would it have been better not to mention it? No, that would have been dishonest. In addition, it is not a crucial point at this very early stage in discovery: this is a new target, and it IS important to obtain information on tighter binding, even if it comes at the cost of heavier molecules. In no way do we pretend that these molecules are ripe for application; we have presented the first set of crude inhibitors to ‘provide inspiration for the design of the next generation of inhibitors’ (last sentence of the paper).

Your blog is widely read and highly respected. In this case, it appears that your analysis was inaccurate due to a case of mistaken identity. I did appreciate your calm and rational tone, and hope that you will agree that there is redeeming value to the poor ligand efficiency, because of the inherent novelty of this discovery effort. I am appealing to you to reconsider the blog’s content in light of the above information, and respectfully request that you consider revising it.

Well, as for DHFRs, I'm guilty as charged. The bacterial ones really are way off the mammalian ones - it appears that dihydro/tetrahydrofolate metabolism is a problem that's been solved a number of different ways and (as is often the case) the bacteria show all kinds of diversity compared to the rest of the living world. And there really aren't any good D67 DHFR inhibitors out there, not selective ones, anyway, so a molecule of that type would definitely be a very worthwhile tool (as well as a potential antibiotic lead).

But that brings us to the fragments, the chemical matter in the paper. I'm going to stand my my characterization of the fragment library. 100 members is indeed small, and claiming lack of access to a "full fragment collection" doesn't quite cover it. Because of the amount of chemical space that can be covered at these molecular weights, a 200-member library can be significantly more useful than a 100-member one, and so on. (Almost anything is more useful than a 100-member library). There aren't more compounds of fragment size on the shelves at the University of Montreal?

More of a case could be made for libraries this small if they covered chemical space well. Unfortunately, looking over the list of compounds tested (which is indeed in the Supplementary Material), it's not, at first glance, a very good collection. Not at all. There are some serious problems, and in a collection this small, mistakes are magnified. I have to point out, to start with, that compounds #59 and #81 are duplicates, as are compounds #3 and #40, and compounds #7 and #14. (There may be others; I haven't made a complete check).

The collection is heavily biased towards carboxylic acids (which is a problem for several reasons, see below). Nearly half the compounds have a COOH group by my quick count, and it's not a good idea to have any binding motif so heavily represented. I realize that you intentionally biased your screening set, but then, an almost featureless hydrophobic compound like #46 has no business in there. Another problem is that some of the compounds are so small that they're unlikely to be tractable fragment hits - I note succinimide (#102) and propyleneurea (#28) as examples, but there are others. At the other end of the scale, compounds such as the Fmoc derivative #25 are too large (MW 373), and that's not the only offender in the group (nor the only Fmoc derivative). The body of the manuscript mentions the molecular weights of the collections as being from 150 to 250, but there are too many outliers. This isn't a large enough collection for this kind of noise to be in it.

There are a number of reactive compounds in the list, too, and while covalent inhibitors are a very interesting field, this was not mentioned as a focus of your efforts or as a component of the screening set. And even among these, compounds such as carbonyldiimidazole (#26), the isocyanate #82, and disuccinimidylcarbonate (#36) are really pushing it, as far as reactivity and hydrolytic stability. The imine #110 is also very small and likely to have hydrolytic stability problems. Finally, the fragment #101 is HEPES, which is rather odd, since HEPES is the buffer for the enzyme assays. Again, there isn't room for these kinds of mistakes. It's hard for me to imagine that anyone who's ever done fragment screening reviewed this manuscript.

The approach to following up these compounds also still appears inadequate to me. As Dan Erlanson pointed out in a comment to the Practical Fragments post, small carboxylic acids like the ones highlighted are not always legitimate hits. They can, as he says, form aggregates, depending on the assay conditions, and the most straightforward way of testing that is often the addition of a small amount of detergent, if the assay can stand it. The behavior of such compounds is also very pH-dependent, as I've had a chance to see myself on a fragment effort, so you need to make sure that you're as close to physiological conditions as you can get. I actually have seen some of your compounds show up as hits in fragment screening efforts, and they've been sometimes real, sometimes not.

But even if we stipulate that these compounds are actually hits, they need more work than they've been given. The best practice, in most cases when a fragment hit is discovered and confirmed, is to take as many closely related single-atom changes into the assay as possible. Scan a methyl group around the structure, scan a fluoro, make the N-for-C switches - at these molecular weights, these changes can make a big difference, and you may well find an even more ligand-efficient structure to work from.

Now, as for the SAR development that actually was done: I understand the point about the symmetry of the enzyme, and I can see why this led to the idea of making symmetrical dimer-type compounds. But, as you know, this isn't always a good idea. Doing so via flexible alkyl or alkyl ether chains is not a good idea, though, since such compounds will surely pay an entropic penalty in binding.

And here's one of the main things that struck both me and Teddy Z in his post: if the larger compounds were truly taking advantage of the symmetry, their ligand efficiency shouldn't go down. But in this case it does, and steeply. The size of the symmetical inhibitors (and their hydrophobic regions, such as the featureless linking chains, make it unsurprising that this effort found some micromolar activity. Lots of things will no doubt show micromolar activity in such chemical space. The paper notes that it's surprising that the fragment 4c showed no activity when its structural motif was used to build some of the more potent large compounds, but the most likely hypothesis is that this is because the binding modes have nothing to do with each other.

To be fair, compounds 8 and 9 are referred to as "poorly optimized", which is certainly true. But the paper goes on to say that they are starting points to develop potent and selective inhibitors, which they're not. The fragments are starting points, if they're really binding. The large compounds are dead ends. That's why Teddy Z and I have reacted as strongly as we have, because the path this paper takes is (to our eyes) an example of how not to do fragment-based drug discovery.

But still, I have to say that I'm very glad to hear a direct reply to my criticism of this paper. I hope that this exchange has been useful, and that it might be of use for others who read it.

Comments (24) + TrackBacks (0) | Category: Drug Assays | Infectious Diseases | The Scientific Literature

April 18, 2012

How Do These Things Get Published?

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Posted by Derek

Update: I've heard from both the lead author of this paper and one of its reviewers, and I've written a follow-up post on this subject, as well as revising this one where shown below.

I've been saved the trouble of demolishing this J. Med. Chem. paper - the Practical Fragments blog has done it for me. I really hate to say such things, but this appears to be one of the worst papers that journal has published in quite a while.

The authors start out with a small, poorly documented (update: the compounds are, in fact, in the paper's supplementary information, but see the follow-up post) library of fragment compounds. They screen these against dihydrofolate reductase, and get a few possible hits - mind you, there's not much correlation between the numbers and any potency against the enzyme, but these aren't potent compounds, and fragment-level hits don't always perform in high-concentration enzyme assays. But what happens next? The authors string these things together into huge dimeric molecules, apparently because they think that this is a good idea, but they get no data to support this hypothesis at all.

Well, their potency goes from low millimolar to low micromolar, but as Teddy Z at Practical Fragments points out, this actually means taking a terrible beating in ligand efficiency. All that extra molecular weight should buy you a lot more potency than this. There's some hand-waving docking of these structures - which the authors themselves refer to as "poorly optimized" - and some inconclusive attempts at X-ray crystallography, leading to uninterpretable data.

And that's it. That's the paper. This on a class of enzymes that's been worked on for decades, yet. (Update: this characterization is completely wrong on my part - see the follow-up post linked to above for more). Again, I hate to be unkind about this, but I cannot imagine what this is doing in J. Med. Chem., or how it made it through the editorial process. When you submit a scientific manuscript for publication, you open yourself to comments from all comers, and those are mine.

Comments (29) + TrackBacks (0) | Category: Infectious Diseases | The Scientific Literature

March 5, 2012

Trouble With a Boron-Containing Drug Candidate

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Posted by Derek

There have been all kinds of boronic acid-based enzyme inhibitors over the years, but they've been mostly locked in the spacious closet labeled "tool compounds". That's as opposed to drugs. After all these years, Velcade is still the only marketed boron-containing drug that I know of.

There's been a good attempt to change that in antibacterials, with the development of what's commonly referred to as "GSK '052", short for GSK2251052. That's a compound that originally came from Anacor about ten years ago, then was picked up by GlaxoSmithKline, and it's an oxaborole heterocycle that inhibits leucyl tRNA synthetase. (Here's a review on that whole idea, if you're interested).
GSK%20052.png
Unfortunately, last month came word that the Phase II trial of the drug had been suspended. All that anyone's saying is that there's a "microbiological finding", which isn't too informative when it's applied to y'know, an antibacterial trial. (At least it doesn't sound like a general safety or tox problem, at any rate).

Anacor is continuing to exploit boron-containing compounds, although opinion looks divided about their prospects. I always have a sneaking fondness for odd compounds and elements, though, so I'd have to root for them just on that basis.

Comments (19) + TrackBacks (0) | Category: Infectious Diseases | Odd Elements in Drugs

February 17, 2012

Hepatitis C: Reality Intrudes

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Posted by Derek

There's been a big drug development story over the last few months that I've been unable to comment on due to conflicts of interest. That situation continues, but I can point to the latest developments, for those who haven't been following the twists and turns.

Comments (29) + TrackBacks (0) | Category: Infectious Diseases

November 30, 2011

The XMRV Story Is Not Getting Any Saner

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Posted by Derek

Dismissals, accusations, possible data theft, and now an arrest - when a scientific hypothesis (and a scientific career) unravels, it unravels all the way. . .

Comments (6) + TrackBacks (0) | Category: Infectious Diseases | The Dark Side

October 18, 2011

Cyclodextrin's Day in the Sun

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Posted by Derek

Under the "Who'da thought?" category, put this news about cyclodextrin. For those outside the field, that's a ring of glucose molecules, strung end to end like a necklace. (Three-dimensionally, it's a lot more like a thick-cut onion ring - see that link for a picture). The most common form, beta-cyclodextrin, has seven glucoses. That structure gives it some interesting properties - the polar hydroxy groups are mostly around the edges and outside surface, while the inside is more friendly to less water-soluble molecules. It's a longtime additive in drug formulations for just that purpose - there are many, many examples known of molecules that fit into the middle of a cyclodextrin in aqueous solution.

But as this story at the Wall Street Journal shows, it's not inert. A group studying possible therapies for Niemann-Pick C disease (a defect in cholesterol storage and handling) was going about this the usual way - one group of animals was getting the proposed therapy, while the other was just getting the drug vehicle. But this time, the vehicle group showed equivalent improvement to the drug-treatment group.

Now, most of the time that happens when neither of them worked; that'll give you equivalence all right. But in this case, both groups showed real improvement. Further study showed that the cyclodextrin derivative used in the dosing vehicle was the active agent. And that's doubly surprising, since one of the big effects seen was on cholesterol accumulation in the central neurons of the rodents. It's hard to imagine that a molecule as big (and as polar-surfaced) as cyclodextrin could cross into the brain, but it's also hard to see how you could have these effects without that happening. It's still an open question - see that PLoS One paper link for a series of hypotheses. One way or another, this will provide a lot of leads and new understanding in this field:

Although the means by which CD exerts its beneficial effects in NPC disease are not understood, the outcome of CD treatment is clearly remarkable. It leads to delay in onset of clinical signs, a significant increase in lifespan, a reduction in cholesterol and ganglioside accumulation in neurons, reduced neurodegeneration, and normalization of markers for both autophagy and neuro-inflammation. Understanding the mechanism of action for CD will not only provide key insights into the cholesterol and GSL dysregulatory events in NPC disease and related disorders, but may also lead to a better understanding of homeostatic regulation of these molecules within normal neurons. Furthermore, elucidating the role of CD in amelioration of NPC disease will likely assist in development of new therapeutic options for this and other fatal lysosomal disorders.

Meanwhile, the key role of cholesterol in the envelope of HIV has led to the use of cyclodextrin as a possible antiretroviral. This looks like a very fortunate intersection of a wide-ranging, important biomolecule (cholesterol) with a widely studied, well-tolerated complexing agent for it (cyclodextrin). It'll be fun to watch how all this plays out. . .

Comments (16) + TrackBacks (0) | Category: Biological News | Infectious Diseases | The Central Nervous System | Toxicology

October 13, 2011

XMRV - Work Went On

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Posted by Derek

I really hesitate to bring this up again, considering the sorts of comments that came in the last time I mentioned XMRV around here. But I wanted to note a new paper that's come out. The authors reveal the crystal structures of the XMRV protease complexed with a number of known inhibitors. Some of them are what you'd expect from homology with similar enzymes, and some have unusual features.

But the details of the structures aren't the main point here - what's worth noting is that they exist. And they took time, and effort, and money to obtain. What's more, this sort of thing also went in several drug companies with an interest in antiviral research, not that any of that work will ever see the light of day, as opposed to this academic publication. Those people accusing the scientific world of callously ignoring the whole area should sit down with these X-ray structures for a few minutes.

No, XMRV was taken seriously by the medical research community, and a lot of serious effort was put into it. That's why it's such a shame that the whole hypothesis has ended up the way it has.

Comments (17) + TrackBacks (0) | Category: Infectious Diseases

October 4, 2011

XMRV: This Is Not Good

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Posted by Derek

If you haven't seen this XMRV news, then you should. The very day after I wrote my most recent post on the subject came this one from ERV over at Scienceblogs.

There are two key figures in it: one from the original Science paper, showing infected patients expressing XMRV Gag protein (a sign of viral infection). And the other was presented recently by Judy Mikovits at a conference in Ottowa. It shows a different experiment - Gag protein being expressed in some other patients only after treatment with 5-azacytidine. The problem is. . .well. . .I'll let you go see for yourselves what the problem is. It most definitely needs explaining, and the explanations had better be good.

Update: continued unraveling. Mikovits herself has been fired from her research institute, apparently for other causes.

Second update: The Chicago Tribune is on this story, breaking it to a wider public. For a link to the alleged third version of the Mikovits figure, see the comments to this post below.

Comments (88) + TrackBacks (0) | Category: Infectious Diseases

September 29, 2011

XMRV: Over With and Done?

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Posted by Derek

Here's an excellent post-mortem on the whole XMRV chronic-fatigue controversy, which I think almost everyone can agree is now at an end. The latest results are from a large blinded effort to detect the virus across a variety of patient sample (and across a number of labs) - and it's negative. The paper that started all the furor has been partially retracted. As far as I can see, the story is over.

But Judy Mikovits of the Whittemore Peterson Institute for Neuro-Immune Disease (WPI) in Nevada, whose work started all this off, is still a believer. And so, as you might imagine, are many patients:

Mikovits has become something of a savior in the community of people with CFS (also known as myalgic encephalomyelitis, or ME), who for decades have endured charges that the disease is psychosomatic. The 2009 Science paper shouted out that CFS may well have a clear biological cause, and, in turn, raised hopes of effective treatments and even a cure. The new findings give her “great pause,” yet she suspects they're but a speed bump. “I haven't changed my thinking at all,” she says. And she worries that the Blood Working Group conclusions will confuse people with CFS, some of whom got wind of the results early in the blogosphere and contacted her in a panic. “I had 15 suicidal patients call me last week,” she says.

In scientific circles, Mikovits has developed a less flattering reputation. Critics have accused her and her backers of stubbornly wedding themselves to a thesis and moving the goalposts with each study that challenges their conclusions. Even disease advocates who welcome the attention XMRV has brought to CFS believe the time has come to put this line of research to rest. “It's hard to say that this has not received a fair appraisal,” says Kimberly McCleary, president of the CFIDS Association of America, a patient group in Charlotte, North Carolina.

At the worst extreme, you get things like this. Note that that post's comment section filled up with people doubting, very vocally, that any such thing was going on, and sometime hinting at big conspiracies to keep the truth from being heard. I'll be a bit disappointed if some more of that doesn't attach to this post as well.

But while I can see why patients in this area are frustrated beyond words, and desperately hoping for something to help them, they're going to have to deal with what every scientist deals with: the indifference of the universe to what we want it to provide. Blind alleys there are beyond counting, wasted effort there is beyond measuring, in trying to understand a disease. We're used to, as humans, seeing agency and design when something seems so well hidden and so complex - in this case, malevolent design. But just as I reject the intelligent design hypothesis to explain what looks benevolent, I reject it for what sometimes looks like an evil practical joke: the perverse difficulties of biomedical research.

Comments (31) + TrackBacks (0) | Category: Infectious Diseases

September 6, 2011

Chronic Fatigue: Enough Energy Left for Death Threats, Anyway

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Posted by Derek

I've written a bit about the struggles to find the biological causes of chronic fatigue syndrome - but perhaps I should shut up? That seems to be the wiser course, given what's reported in this piece from the UK:

The full extent of the campaign of intimidation, attacks and death threats made against scientists by activists who claim researchers are suppressing the real cause of chronic fatigue syndrome is revealed today by the Observer. According to the police, the militants are now considered to be as dangerous and uncompromising as animal rights extremists.

One researcher told the Observer that a woman protester who had turned up at one of his lectures was found to be carrying a knife. Another scientist had to abandon a collaboration with American doctors after being told she risked being shot, while another was punched in the street. All said they had received death threats and vitriolic abuse.

The crime these people have committed, according to the various unhinged activists, is that they're suggesting that there could perhaps be a psychological component to the condition, or even just that the various proposals put forth for a viral cause don't seem to be holding up well. And we jump from that to death threats, harassment, calls for defunding, and accusations of dark deeds underwritten by Evil Pharmaceutical Companies.

That last one is especially weird, as one of the interviewees in the article makes clear. If there were a definite viral cause for chronic fatigue and allied syndromes, we Evil Pharma Scientists would do what we've done so evilly for HIV, hepatitis, and other diseases: come up with drugs to treat people or (better yet) vaccines to try to keep anyone from ever getting the disease again. Dark stuff indeed.

Comments (38) + TrackBacks (0) | Category: Infectious Diseases | The Dark Side

August 26, 2011

Kibdelomycin, A New Antibiotic. In A Way.

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Posted by Derek

We're going to need new antibiotics. Everyone knows this, and it's not like no one's been trying to do anything about it, either, but. . .we're still going to need more of them than we have. I'm not predicting that we're going to go all the way back to a world where young, healthy people with access to the best medical care die because they decided to play tennis without their socks on, but we're certainly in danger of a much nastier world than we have.

So I'm always interested to hear of new antibiotic discovery programs, and Merck is out with an interesting paper on theirs. They've been digging through the natural products, which have been the fount from which almost all antibiotics have sprung, and they have a new one called kibdelomycin to report. This one was dug out from an organism in a sample from the Central African Republic by a complicated but useful screening protocol, the S. aureus fitness test. This relies on 245 different engineered strains of the bacterium, each with an inducible RNAi pathway to downregulate some essential gene. When you pool these into mixed groups and grow them in the presence of test compounds (or natural product extracts) for 20 generations or so, a check of what strains have moved ahead (and fallen behind) can tell you what pathways you seem to be targeting. A key feature is that you can compare the profile you get with those of known antibiotics, so you don't end up rediscovering something (or discovering something that only duplicates what we already have anyway).
Kibdelomycin.png Now, that's no one's idea of a beautiful structure, although (to be fair) a lot of antibiotics have very weird structures themselves. But it's safe to say that there are some features there that could be trouble in a whole animal, such as that central keto-enol-pyrrolidone ring and the funky unsaturated system next to it. (The dichloropyrrole, though, is interestingly reminiscent of these AstraZeneca gyrase/topoisomerase antibiotic candidates, while both celestramycin and pyoluteorin have a different dichloropyrrole in them).

What kind of activity does kibdelomycin have? Well, this is where my enthusiasm cools off just a bit more. It showed up in screening with a profile similar to the coumarin antibiotics novobiocin and chlorobiocin, and sure enough, it's a topoisomerase II inhibitor. It appears to be active almost entirely on gram-positive organisms. And while there are certainly nasty gram-positive infections that have to be dealt with, I'm more encouraged when I see something that hits gram-negatives as well. They've got more complicated defenses, those guys, and they're harder to kill. It's not easy to get broad-spectrum activity when you're going after gyrase/Topo II, but the fluoroquinolones definitely manage it.

The Merck team makes much out of kibdelomycin being "the first truly novel bacterial type II topoisomerase inhibitor with potent antibacterial activity discovered from natural product sources in more than six decades". And they're right that this is an accomplishment. But the kicker in that sentence is "from natural product sources". Getting gram-positive Topo II inhibitors has actually been one of the areas where synthetic compounds have had the most success. Building off the quinolones themselves has been a reasonably fruitful strategy, and a look through the literature turns up a number of other structural classes with this sort of activity (including some pretty wild ones). Not all of these are going places, but there are certainly a number of possibilities out there.

In short, if kibdelomycin weren't an odd-looking natural product, I wonder how much attention another high-molecular-weight gram-positive-only topoisomerase inhibitor would be getting, especially with only in vitro data behind it. Every little bit helps, and having a new structural class to work from is a worthwhile discovery. But one could still want (and hope) for more.

Comments (14) + TrackBacks (0) | Category: Drug Assays | Infectious Diseases | Natural Products

August 22, 2011

DRACOs: New Antivirals Against Pretty Much Everything?

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Posted by Derek

I've been meaning to write about this paper from the RIder group at MIT's Lincoln Labs, which shows some very interesting approaches to killing off a wide variety of viruses. They've dubbed these new agents DRACOs, for Double-stranded RNA Activated Caspase Oligimerizers, which is certainly one of those acronyms with a lot packed into it.

So now to unpacking it. The first key point is the double-stranded RNA (dsRNA) part. For a long time, that was thought to be a form that isn't wasn't found in human cells (as opposed to single-stranded stuff). We now know that short dsRNAs (up to twenty-odd base pairs) are part of human biology, but viruses produce much longer strands of it during their replication process - or, more accurately, they hijack human cellular machinery to produce it. (Viruses, as a rule, don't do anything for themselves that they don't absolutely have to).

Naturally enough, cells have evolved ways to recognized long dsRNAs as a sign of infection - there's a whole list of proteins that recognize these things and bind to them. Some of them inhibit its downstream processing directly, by just hanging on and gumming up the works, while others set off responses further downstream. One of those is apoptosis, programmed cell death, a brutal but effective fall-on-your-sword pathway that gets initiated by all sorts of unfixable cellular problems. (When a cell's internal controls give a "Fatal Error" message, it's taken literally). And naturally enough, viruses have evolved ways to try to evade these defenses, both by targeting the dsRNA detection proteins and by inhibition of apoptosis pathways. (As a side note, it's always been interesting to untangle these counter-counter-countermeasure situations whenever a new cellular pathway relating to infection is worked out. You find, invariably, that hundreds of millions of years of evolutionary pressure have built up crazily elaborate frameworks around all of them).

This approach tries to speed up the dsRNA-means-apoptosis connection. A DRACO turns out to be a good-sized protein with two functions: one end recognizes and binds to dsRNA, and the second contains a signal to induce apotosis. If multiple copies of the DRACO protein stick to the same viral dsRNA strand, that should be enough to initiate cell death and interrupt the viral replication process. The team tried out a whole range of possibilities for both those functional domains, with the best (so far) using either Protein Kinase R (PKR) or RNAaseL domains to recognize viral RNA and an Apaf caspase recruitment domain for apoptosis signaling. Another key modification was the addition of a PTD (protein transduction domain) tag, which allows large proteins like these entry into cells through active transport. (Cells only take in whole proteins through gatekeeping transport mechanisms; otherwise they just sort of bounce off - this effect was confirmed with DRACOs that lacked the PTD tags).

So, basically, this is the sort of protein that you might expect evolution to stumble onto eventually, but now the connecting line has been drawn by hand instead. It's worth noting at this point, though, that this general idea has occurred to others before: here's a paper from Boston University trying the same sort of strategy. That one was published online in 2009, but didn't make it to print until May of this year, which makes you wonder if that's a typical delay for that journal (FASEB J.) or not. It's also worth noting that, for whatever reason, this new MIT paper does not cite the one from BU.

How did they work? Pretty well. The PTD tags did what they were supposed to, taking the proteins into cells rapidly. Once inside, the DRACOs themselves hung around for several days before being degraded, which is another big hurdle. And they did indeed protect against infection by an impressively wide range of viruses in cell culture: rhinovirus, encephalomyelitis, adenoviruses, arenaviruses, bunyaviruses, flaviviruses, reovirus, and flu. A lot of nasty pathogens fall into those bins.

But that's in cell culture, which is a long way from a living organism. To their credit, the team went on to try out their idea in live mice, and they show some encouraging results. Administering their best DRACO candidates to mice and then exposing them to influenza virus took the survival rate (at ten days) from under 10% in the control groups up to 60-70% survival for the PKR version and up to 100% survival for the RNAaseL version.

It's an impressive graph, but there are some things to note about it. For one, the DRACO proteins were administered by injection - these are probably never going to be feasible as oral medications, since they're large proteins which will just get digested. But again to their credit, the MIT group also tested dosing via intranasal injection (yep, squirting the protein solution up the noses of mice, truly the glamorous end of science). That also showed a strong protective effect after influenza virus exposure, which is a good sign.

Now comes the next concern. You might have already wondered about my mention of the injection route, since we already give millions of people a year injections to combat viral infection: flu shots. Those, though, are vaccines meant to last the whole season (and beyond). DRACO proteins get cleared out in mice on a time scale of days; they wouldn't be expected to have any long-range immune effects. (Of course, their broad antiviral effects, versus the sometimes way-too-specific nature of a vaccine, is a strong point in their favor). But this brings up another issue that's going to have to be addressed: when you look at the graphs of the mice experiments, you note that the DRACOs were given either on Day 0 or Day -1 compared to the exposure to virus.

That's actually a big deal in this field. The problem with antiviral therapies has always been that you don't usually know that you've been infected until, well, after you've been infected. Sometimes that lag time is rather long, and it's always long enough for the virus to get a good running start. Symptoms, after all, don't occur until things are well under way. In the real world, the two opportunities for antiviral therapies are (1) something that you can take long before you're even exposed, and that lasts for a long time (like a vaccine) or (2) something that you can take after you've already realized that you're sick (like an antiviral drug). So far, the DRACO proteins fall in between these two, and the next challenge for these agents is to see if they can stretch into one or the other. The authors, no fools, realize this:

Based on these encouraging initial animal trials, future work should be done to test and optimize antiviral efficacy, pharmacokinetics, and absence of toxicity in vitro and in vivo. Future experiments can further characterize and optimize dsRNA binding, apoptosis induction, cellular transduction, and other DRACO properties. More extensive trials are also needed to determine how long after infection DRACOs can be used successfully, or if DRACOs are useful against chronic viral infections without producing unacceptable levels of cell death in vivo.

It's going to be very interesting to see how this field develops. It's a promising start, for sure, but there are still a lot of ways for things not to work out. Just getting this far along in the "promising start" phase is a real accomplishment, though, and more than many people have ever been able to manage.

Comments (15) + TrackBacks (0) | Category: Infectious Diseases

June 27, 2011

The Evolution of Resistance: Are We Doing It Wrong?

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Posted by Derek

Here's a paper in PNAS that says that we're probably treating infectious disease the wrong way - and perhaps cancer as well. The authors go over the currently accepted doctrines: multiple-mechanism therapies, when possible, and restricted use to patients who really need antibiotics. But there's a third assumption that they say is causing trouble:

A third practice thought to be an effective resistant management strategy is the use of drugs to clear all target pathogens from a patient as fast as possible. We hereafter refer to this practice as “radical pathogen cure.” For a wide variety of infectious diseases, recommended drug doses, interdose intervals, and treatment durations (which together constitute “patient treatment regimens”) are designed to achieve complete pathogen elimination as fast as possible. This is often the basis for physicians exhorting their patients to finish a drug course long after they feel better (long-course chemotherapy). Our claim is that aggressive chemotherapy cannot be assumed to be an effective resistance management strategy a priori. This is because radical pathogen cure necessarily confers the strongest possible evolutionary advantage on the very pathogens that cause drugs to fail.

The harder you hit a population of infectious disease organisms, the harder you're selecting for resistance. The key, they say, is that in many cases there's genetic diversity among these organisms even inside single patients. So you can start off with a population of bacteria, say, that could be managed by less aggressive therapy and the patient's own immune system. But then aggressive treatment ends up killing off the great majority of the bacterial population, which you'd think would be a step forward. But what you're left with are the genotypes that are hardest to kill with antibiotics. They were in a minority, and might well have died out under competition from their less-genetically-burdened cohorts. But killing those off gives the resistant organisms an open field to work in.

The other problem here is a public-heath one. You want to cure the individual patient, and you want to keep their disease from spreading, and you want to keep from encouraging resistance among the infectious organisms. Optimizing for all three at once is probably not possible.

The paper goes into detail with the example of malaria, pointing out that it may well be the norm for people to be infected with several different lineages of malaria parasites at the same time. They seem to be in there competing for nutrients and for red blood cells, and some of them appear to be keeping the others in check. Antimalarial drugs alter the cost/benefit ratio (for the parasites) of carrying resistance genes.

So what should we do? The problem is, they say, that there are probably no general rules that can be recommended:

Thus, aggressive chemotherapy is a double-edged sword for resistance management. It can reduce the chances of high-level resistance arising de novo in an infection. But when an infection does contain resistant parasites, either from de novo mutation or acquired by transmission from other hosts, it gives those parasites the greatest possible evolutionary advantage both within individual hosts and in the population as a whole. How do the opposing evolutionary pressures generated by radical cure combine in different circumstances to determine the useful life span of a drug? There will be circumstances when overwhelming chemical force retards evolution and other times when it drives things very rapidly. We contend that for no infectious disease do we have sufficient theory and empiricism to determine which outcome is more important. It seems unlikely that any general rule will apply even for a single disease, let alone across disease systems.

For more on such ideas as applied to bacterial infections, see here and here. But near the end of this paper, the authors apply similar reasoning to cancer. (That analogy has come up around here before, I should note).

An analogous situation also occurs in cancer therapy, where cell lineages within a tumor compete for access to space and nutrients. There, the argument has recently been made that less aggressive chemotherapy might sustain life better than overwhelming drug treatment, which simply removes the competitively more able susceptible cell lineages, allowing drug-resistant lineages to kill the host. Mouse experiments support this: Conventionally treated mice died of drug-resistant tumors, but less aggressively treated mice survived (95).

So maybe too many of us have been thinking about these questions the wrong way. If we switch over to favoring whatever strategy minimizes resistance, both in individual patients and thus across the population, we could be in better shape. . .

Comments (21) + TrackBacks (0) | Category: Cancer | Infectious Diseases

June 7, 2011

Murine Viruses and Chronic Fatigue: Does the Story Continue

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Posted by Derek

Well, one day after writing an obit for the XMRV story comes this abstract from Retrovirology. The authors, from Cornell and SUNY-Buffalo, say that they've detected other murine retrovirus transcripts from CFS patients (but not in most controls), and that these are more similar to those reported in last year's Lo and Alter paper in PNAS than they are to XMRV itself.

So perhaps the story continues, and what a mess it is at this point. I continue to think that the XMRV hypothesis itself is in serious trouble, but murine retroviruses as a class are still worth following up on. This is tough work, though, because of the twin problems of detection and contamination, and it's going to be easy for people to fool themselves.

Meanwhile, Retraction Watch has more on Science's "Expression of Concern" that I wrote about yesterday. It appears that the journal asked the authors to retract the paper (so says the Wall Street Journal, anyway) but that co-author Judy Mikovits turned them down (as might have been expected from her previous stands in this area). Science released their editorial note early because of the WSJ piece.

Comments (15) + TrackBacks (0) | Category: Infectious Diseases | The Scientific Literature

June 6, 2011

XMRV and Chronic Fatigue: Down For More Than the Third Time

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Posted by Derek

I meant to blog on this late last week, but (in case you haven't seen it) the whole putative link between XMRV and chronic fatigue syndrome seems now to be falling apart. If you want to see the whole saga via my blog posts and the links in them, then here you go: October 2009 - January 2010 - February 2010 - July 2010 - January 2011. At that last check-in, the whole thing was looking more like an artifact.

And now Science is out with a paper that strongly suggests that the entire XMRV virus is an artifact. It looks like something that's produced by the combination of two proviruses during passaging of the cells where it was detected, and the paper suggests that other human-positive samples are the result of contamination. Another paper is (again) unable to replicate detection of XMRV in dozens of samples which had previously been reported as positive, and finds some low levels of murine virus sequences in commercial reagents, which also fits with the contamination hypothesis.

With these results in print, Science has attached an "Editorial Expression of Concern" to the original 2009 XMRV/CFS paper, which touched off this whole controversy. My take: while there are still some studies ongoing, at this point it's going to take a really miraculous result to bring this hypothesis back to life. It certainly looks dead from here.

There will be also be some people who ask whether Science did the world a favor by publishing the original paper in the first place. But on balance, I'd rather have things like this get published than not, although in hindsight it's always easy to say that more experiments should have been done. The same applies to the arsenic-bacteria paper, another one of Science's recent bombshells. I'm not believing that one, either, at this point - not until I see a lot more supporting data - but in the end, I'm not sad that it was published, either. I think we're better off erring a bit on the wild-ideas end of the scale than clamping down too hard. That said, you do have to wonder if Science in particular is pushing things a bit too hard, itself. While I think that these ideas deserve a hearing, it doesn't necessarily have to be there.

Comments (18) + TrackBacks (0) | Category: Infectious Diseases | The Scientific Literature

May 13, 2011

Process Chemistry Makes the Headlines

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Posted by Derek

Not a common occurrence, that. But this Wall Street Journal article goes into details on some efforts to improve the synthetic route to Viread (tenofovir) (or, to be more specific, TDF, the prodrug form of it, which is how it's dosed). This is being funded by former president Bill Clinton's health care foundation:

The chasm between the need for the drugs and the available funding has spurred wide-ranging efforts to bring down the cost of antiretrovirals, from persuading drug makers to share patents of antiretrovirals to conducting trials using lower doses of existing drugs.

Beginning in 2005, the Clinton team saw a possible path in the laboratory to lowering the price of the drugs. Mr. Clinton's foundation had brokered discounts on first-line AIDS drugs, many of which were older and used relatively simple chemistry. Newer drugs, with advantages such as fewer side effects, were more complex and costly to make. . .A particularly difficult step in the manufacture of the antiretroviral drug tenofovir comes near the end. The mixture at that point is "like oatmeal, making it very difficult to stir," explained Prof. Fortunak. That slows the next reaction, a problem because the substance that will become the drug is highly unstable and decomposing, sharply lowering the yield.

Fortunak himself is a former Abbott researcher, now at Howard University. One of his students does seem to have improved that step, thinning out the reaction mixture (which was gunking up with triethylammonium salts) and improving the stability of the compound in it. (Here's the publication on this work, which highlights that step, formation of a phosphate ester, which is greatly enhanced with addition of tetrabutylammonium bromide). This review has more on production of TDF and other antiretrovirals.

This is a pure, 100% real-world process chemistry problem, as the readers here who do it for a living will confirm, and it's very nice to see this kind of work get the publicity that it deserves. People who've never synthesized or (especially) manufactured a drug generally don't realize what a tricky business it can be. The chemistry has to work on large scale (above all!), and do so reproducibly, hitting the mark every time using the least hazardous reagents possible, which have to be reliably sourced at reasonable prices. And physically, the route has to avoid extremes of temperature or pressure, with mixtures that can be stirred, pumped from reactor to reactor, filtered, and purified without recourse to the expensive techniques that those of us in the discovery labs use routinely. Oh, and the whole process has to produce the least objectionable waste stream that you can come up with, too, in case you've got all those other factors worked out already. Not an easy problem, in most cases, and I wish that some of those people who think that drug companies don't do any research of their own would come down and see how it's done.

To give you an example of these problems, the paper on this tenofovir work mentions that the phosphate alkylation seems to work best with magnesium t-butoxide, but that the yield varies from batch to batch, depending on the supplier. And in the workup to that reaction, you can lose product in the cake of magnesium salts that have to be filtered out, a problem that needs attention on scale.

According to the article, an Indian generic company is using the Howard route for tenofovir that's being sold in South Africa. (Tenofovir is not under patent protection in India). Interestingly, two of the big generic outfits (Mylan and Cipla) say that they'd already made their own improvements to the process, but the question of why that didn't bring down the price already is not explored. Did the Clinton foundation improve a published Gilead route that someone else had already fixed? Cipla apparently does the same phosphate alkylation (PDF), but the only patent filing of theirs that I can find that addresses tenofovir production is this one, on its crystalline form. Trade secret?

Comments (21) + TrackBacks (0) | Category: Chemical News | Drug Development | Drug Prices | Infectious Diseases

April 15, 2011

Selenium In a Drug Structure: Why Not?

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Posted by Derek

You don't see too many drugs with selenium in them, that's for sure. It's one of those elements that can be used to illustrate the Paracelsian doctrine that the dose makes the poison: selenium is an essential element that's also toxic. There's no doubt at all about either of those properties; it all depends on how much of it you get.

And that's the problem with using the element in a drug molecule - the dose of many pharmaceuticals would then exceed the safe amount of selenium that a person could take in. That's especially true for whopping-dose areas like antibiotics (Home of the Horse Pill reads the sign over the door). So it's especially interesting to see that Achillion has spent some time and effort developing just that: a new antibiotic candidate whose essential feature is a selenium substitution.

No, they're not idiots. In fact, I have to salute them for having the nerve to go down this path. The key here is that the selenium in tied up in a heterocycle, a selenophene (analogous to thiophene, and not a heterocycle that very many chemists will have seen.) This keeps the element from being bioavailable, as is apparently the case with the even stranger heterocycle ebselen.
selenophene%2Cjpg.jpg
And going from a thiophene to a selenophene is not a neutral switch - in this case, it seems to have been quite helpful. The structures are in a family of topoisomerase/gyrase inhibitors that have shown a lot of promise, but have dropped out of development due to potential cardiac side effects. It's the dreaded hERG channel again, which has sunk many a development program. Binding to that ion channel can lead to long QT syndrome in some patients, and you really don't want that risk. (Neither do the regulatory agencies, which require testing of any new drug candidate for just this reason).

Switching to selenophene gave the cleanest hERG profile for Achillion's entire series of compounds, while still retaining antibacterial activity. So these selenium heterocycles are, for the adventurous, probably worth a look - they can be similar to thiophene in some situations, and not so similar in others. People are going to look at you funny if you make them, but you should never let that slow you down.

Comments (30) + TrackBacks (0) | Category: Infectious Diseases | Odd Elements in Drugs

March 16, 2011

Pfizer Moves Antibacterials to Shanghai

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Posted by Derek

So Pfizer has announced that their antibacterial research is moving to the Shanghai site. Is this the first example of a large/traditional therapeutic area moving to China? And if it is, should we care? After all, there are Swiss, German, British, and Japanese companies, among others, with multinational research sites. Some programs run at one facility, and some at another. When you add China to that list, though, something happens for a lot of people.

That's because the Chinese sites got their start as the inexpensive way to offshore work, for one thing. But Shanghai's not as cheap as it used to be - it's still less expensive than doing the work in the US or western Europe, but the cost advantage is eroding. Another factor is that you don't see companies expanding into new therapeutic areas these days, so much as moving the existing ones around. In that zero-sum game, expanding one site means contracting another.

Here's something to think about, though: does Pfizer's choice here represent a calculation about some future opportunity in China, should they be able to develop any drugs? Would the "discovered and developed in Shanghai" factor help with the regulatory authorities there?

Comments (37) + TrackBacks (0) | Category: Business and Markets | Infectious Diseases

January 11, 2011

XMRV: It's Ugly, But That's Science

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Posted by Derek

How's the XMRV / chronic fatigue syndrome connection holding up? Not real well. Science has a roundup of the latest news in the area, and none of it looks encouraging. There are four studies that have come out in the journal Retrovirology that strongly suggest that earlier positive test results for the virus in CFS samples are just artifacts.

For one thing, when you look closely, it turns out that the sequences from cell-cultured XMRV samples are quite a bit more diverse than the ones taken from widely separated patients at different times. And that's just not right for an infectious agent; it's the opposite of what you should see. A number of supposedly XMRV-specific primers that have been used in such assays also appear to amplify other murine viral sequences as well, and samples that show positive for XMRV also appear to have some mouse DNA in them. Finally, there's reason to believe that some common sources of PCR reagents may have murine viral contaminants that blow up this particular assay.

Taken together, these latest results really have to make you cautious in assigning any role at all to XMRV based on the published data. You can't be sure that any of the numbers are what they're supposed to be, and the most parsimonious explanation is that the whole thing has been a mistake. To illustrate the state of things, you may remember an effort to have several labs (on both sides of the issue) test the same set of samples. Well, according to Science. . .

Some had hoped that a project in which several U.S. labs are testing for XMRV in the same samples would clear up the picture. But so far this effort has been inconclusive. Four CFS patients' blood initially tested positive for XMRV at WPI and the U.S. Centers for Disease Control and Prevention but not at an NCI lab. When all three labs tested new samples from the same patients, none found XMRV—for reasons that aren't yet clear, says Coffin. The group now plans to test blood from several dozen CFS patients and controls.

No, this isn't looking good at all. It's pretty typical, though, of how things are out at the frontiers in this business. There are always more variables than you think, and more reasons to be wrong than you've counted. A theory doesn't hold up until everyone who wants to has had a chance to take some big piñata-shattering swings at it, with weapons of their choice. So, to people outside of research: you're not seeing evidence of bad faith, conspiracy, or stupidity here. You're seeing exactly how science gets done. It isn't pretty, but it gets results in the end. Circumspice.

Comments (70) + TrackBacks (0) | Category: Analytical Chemistry | Infectious Diseases

December 15, 2010

Chiral What? Chiral How?

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Posted by Derek

Thanks to an email from a reader, I can bring you this very weird paper from Tetrahedron. The authors claim to have extracted a local plant and isolated nevirapine, (sold as Viramune by Boehringer Ingleheim as a reverse transcriptase inhibitor for HIV).
nevirapine.png
That's kind of odd. I'm no natural products expert, but I've sure seen a lot of them over the years, and that framework (and the N-cyclopropyl) don't look so likely to me. But hey, plants do odd things. That's not what's really puzzling about this paper. No, what's had me staring at it this morning is the claim that, in contrast to the marketed drug, this stuff is optically active nevirapine.

Say what? Try as I might, I can't see any plausible way that that's a chiral compound. The authors seem to think it is, though. They claim optical rotation, somehow, and then say that "The detailed structure and stereochemistry of compound 1 was established unambiguously by single crystal X-ray crystallography." But hold on - that's not as easy as it sounds. Getting absolute configurations from the X-ray data of light-atom-only molecules takes special efforts, and I don't see any being taken (molybdenum X-rays, direct methods, no talk of anomalous dispersion, etc.)

I'm just not willing to see that nitrogen atom as a source of chirality - if it were, shouldn't that be the focus of this whole paper? Instead, the authors just blithely tell us how neat it is that they've isolated the chiral material. In fact, they find it so neat that they tell us two times in a row:

This is a very interesting discovery that naturally occurring optically active nevirapine has been biosynthesized in the seeds of C.viscosa and the optically inactive nevirapine was designed as a selective non-nucleoside inhibitor of HIV-1 reverse transcriptase. It is also a remarkable finding that the seed of C.viscosa is the source of optically active nevirapine, which was also designed and synthesized before its isolation from natural source.

This sounds like some sort of lunatic patent-busting exercise, to be honest. And it sounds as if someone doesn't know what a chiral compound is. And that whoever reviewed this for Tetrahedron was incompetent. And that the editor who let it through should be a least a little bit ashamed. Well?

Comments (73) + TrackBacks (0) | Category: Infectious Diseases | Natural Products | The Scientific Literature

December 2, 2010

HIV Therapies: A Thank-You

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Posted by Derek

A rare op-ed note of appreciation for the drug industry: who would have predicted, 20 years ago, that the viral disease for which we have the widest range of effective therapies would be HIV?

Comments (20) + TrackBacks (0) | Category: Infectious Diseases

November 3, 2010

TRIM21: A Cure For the Common Cold? Maybe Not. . .

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Posted by Derek

This article is getting the "cure for the common cold" push in a number of newspaper headlines and blog posts. I'm always alert for those, because, as a medicinal chemist, I can tell you that finding a c-for-the-c-c is actually very hard. So how does this one look?

I'd say that this falls into the "interesting discovery, confused reporting" category, which is a broad one. The Cambridge team whose work is getting all the press has actually found something that's very much worth knowing: that antibodies actually work inside human cells. Turns out that when antibody-tagged viral particles are taken up into cells, they mark the viruses for destruction in the proteosome, an organelle that's been accurately compared to an industrial crushing machine at a recycling center. No one knew this up until now - the thought had been that once a virus succeeds in entering the cell, that the game was pretty much up. But now we know that there is a last line of defense.

Some of the press coverage makes it sound as if this is some new process, a trick that cells have now been taught to perform. But the point is that they've been doing it all along (at least to nonenveloped viruses with antibodies on them), and that we've just now caught on. Unfortunately, that means that all our viral epidemics take place in the face of this mechanism (although they'd presumably be even worse without it). So where does this "cure for the common cold" stuff come in?

That looks like confusion over the mechanism to me. Let's go to the real paper, which is open-access in PNAS. The key protein in this process has been identified as tripartite-motif 21 (TRIM21), which recognized immunoglobin G and binds (extremely tightly, sub-nanomolar) to antibodies. This same group identified this protein a few years ago, and found that it's highly conserved across many species, and binds an antibody region that never changes - strong clues that it's up to something important.

Another region of TRIM21 suggested what that might be. It has a domain that's associated with ubiquitin ligase activity, and tagging something inside the cell with ubiquitin is like slapping a waste-disposal tag on it. Ubiquinated proteins tend to either get consumed where they stand or dragged off to the proteosome. And sure enough, a compound that's known to inhibit the action of the proteosome also wiped out the TRIM21-based activity. A number of other tests (for levels of ubiquitination, localization within the cell, and so on) all point in the same direction, so this looks pretty solid.

But how do you turn this into a therapy, then? The newspaper articles have suggested it as a nasal spray, which raises some interesting questions. (Giving it orally is a nonstarter, I'd think: with rare exceptions, we tend to just digest every protein that gets into the gut, so all a TRIM21 pill would do is provide you with a tiny (and expensive) protein supplement). Remember, this is an intracellular mechanism; there's presumably not much of a role for TRIM21 outside the cell. Would a virus/antibody/TRIM21 complex even get inside the cell to be degraded? On the other hand, if that kept the virus from even entering the cell, that would be an effective therapy all its own, albeit through a different mechanism than ever intended.

But hold on: there must be some reason why this mechanism doesn't always work perfectly - otherwise, no nonenveloped virus would have much of a chance. My guess is that the TRIM21 pathway is pretty efficient, but that enough viral particles miss getting labeled by antibodies to keep it from always triggering. If that's true, then TRIM21 isn't the limiting factor here - it's antibody response. If that's true, then it could be tough to rev up this pathway.

Still, these are early days. I'm very happy to see this work, because it shows us (again) how much we don't know about some very important cellular processes. Until this week, no one ever realized that there was such a thing as an intracellular antibody response. What else don't we know?

Comments (12) + TrackBacks (0) | Category: Biological News | Infectious Diseases

August 24, 2010

XMRV? Or Umpteen Other Viruses? Or What?

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Posted by Derek

The long-delayed PNAS paper on the chronic fatigue/XMRV results has finally come out. It's not going to stop the arguing.

From what I can see, this team didn't find "canonical" XMRV in the samples from CFS patients. But what they did find was a whole slew of similar-looking traces of murine leukemia viruses (MLVs). (The samples do not appear to have been contaminated, which is the first thing you'd wonder about).

So now we're back to more head-scratching. Is XMRV a culprit at all, or is it some other related MLV? Or is it, instead, several of them at the same time? How many people without symptoms show the same MLV signs anyway? And so on. It's clear that this story is nowhere near over. It's only barely starting. . .

Here's the PNAS commentary on the article, which adds some clarity. But no one's got enough clarity on hand for this subject yet.

Comments (13) + TrackBacks (0) | Category: Infectious Diseases

August 3, 2010

Know How to Make Praziquantel? Tell The World.

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Posted by Derek

One of the people I met this past weekend was Matt Todd, chemistry professor at the University of Sydney. We talked about a project his lab is working on, and I wanted to help call attention to it.

They're working on praziquantel, also known as PZQ or Biltricide, which is used to cure schistosomiasis in the tropics. It's on the WHO's list of essential medicines for this reason. But PZQ is used now as a racemate, and this is one of those cases where everyone would be better off with a single enantiomer - not least, because the active enantiomer is significantly easier for patients to stand than the racemic mixture. Problem is, there's no cheap enantioselective synthesis or resolution.

So what Todd's group has done is crowdsourced the problem. Here's the page to start with, where they lay out the current synthetic difficulties - right now, those include enantioselective Pictet-Spengler catalysts and help with the resolution of a key intermediate. They were in need of chiral HPLC conditions, but that problem has recently been solved. I'd like to ask the chemists in the crowd here to take a look, because it wouldn't surprise me if one of us had some ideas that could help. Don't leave your suggestions here, though; do it over at their pages so it's all in one place.

This sort of thing is an excellent fit with open-source models for doing science: it's all pro bono, and the more eyes that take a look at the situation, the better the chance that a solution will emerge. I don't think it's getting the publicity it deserves. And no, in case anyone's wondering, I don't think that this is how we're all going to end up discovering drugs. Figuring out how to do this for large commercial projects tends to bring on frantic hand-waving. But in cases like this - specific problems where there's no chance for profit to push things along - I think it can work well. It makes a lot more sense than that stuff I was linking to last week!

Comments (22) + TrackBacks (0) | Category: Business and Markets | Chemical News | General Scientific News | Infectious Diseases

July 7, 2010

XMRV and Chronic Fatigue: You Thought You Were Confused Before

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Posted by Derek

Time to revisit the chr