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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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August 14, 2014

Proteins Grazing Against Proteins

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Posted by Derek

A huge amount of what's actually going on inside living cells involves protein-protein interactions. Drug discovery, for obvious reasons, focuses on the processes that depend on small molecules and their binding sites (thus the preponderance of receptor ligands and enzyme inhibitors), but small molecules are only part of the story in there.

And we've learned a fair amount about all this protein-protein deal-making, but there's clearly a lot that we don't understand at all. If we did, perhaps we'd have more compounds that can target them. Here's a very basic topic about which we know very little: how tight are the affinities between all these interacting proteins? What's the usual level, and what's the range? What does the variation in binding constants say about the signaling pathways involved, and the sorts of binding surfaces that are being presented? How long do these protein complexes last? How weak can one of these interactions be, and still be physiologically important?

A new paper has something to say about that last part. The authors have found a bacterial system where protein phosphorylation takes place effectively although the affinity between the two partners (KD) is only around 25 millimolar. That's very weak indeed - for those outside of drug discovery, small-molecule drug affinities are typically well over a million times that level. We don't know how common or important such weak interactions are, but this work suggests that we're going to have to look pretty far up the scale in order to understand things, and that's probably going to require new technologies to quantify such things. Unless we figure out that huge, multipartner protein dance that's going on, with all its moves and time signatures, we're not going to understand biochemistry. The Labanotation for a cell would be something to see. . .

Comments (4) + TrackBacks (0) | Category: Biological News | Chemical Biology

July 18, 2014

Thalidomide, Bound to Its Target

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Posted by Derek

There's a new report in the literature on the mechanism of thalidomide, so I thought I'd spend some time talking about the compound. Just mentioning the name to anyone familiar with its history is enough to bring on a shiver. The compound, administered as a sedative/morning sickness remedy to pregnant women in the 1950s and early 1960s, famously brought on a wave of severe birth defects. There's a lot of confusion about this event in the popular literature, though - some people don't even realize that the drug was never approved in the US, although this was a famous save by the (then much smaller) FDA and especially by Frances Oldham Kelsey. And even those who know a good amount about the case can be confused by the toxicology, because it's confusing: no phenotype in rats, but big reproductive tox trouble in mice and rabbits (and humans, of course). And as I mentioned here, the compound is often used as an example of the far different effects of different enantiomers. But practically speaking, that's not the case: thalidomide has a very easily racemized chiral center, which gets scrambled in vivo. It doesn't matter if you take the racemate or a pure enantiomer; you're going to get both of the isomers once it's in circulation.

The compound's horrific effects led to a great deal of research on its mechanism. Along the way, thalidomide itself was found to be useful in the treatment of leprosy, and in recent years it's been approved for use in multiple myeloma and other cancers. (This led to an unusual lawsuit claiming credit for the idea). It's a potent anti-angiogenic compound, among other things, although the precise mechanism is still a matter for debate - in vivo, the compound has effects on a number of wide-ranging growth factors (and these were long thought to be the mechanism underlying its effects on embryos). Those embryonic effects complicate the drug's use immensely - Celgene, who got it through trials and approval for myeloma, have to keep a very tight patient registry, among other things, and control its distribution carefully. Experience has shown that turning thalidomide loose will always end up with someone (i.e. a pregnant woman) getting exposed to it who shouldn't be - it's gotten to the point that the WHO no longer recommends it for use in leprosy treatment, despite its clear evidence of benefit, and it's down to just those problems of distribution and control.

But in 2010, it was reported that the drug binds to a protein called cereblon (CRBN), and this mechanism implicated the ubiquitin ligase system in the embryonic effects. That's an interesting and important pathway - ubiquitin is, as the name implies, ubiquitous, and addition of a string of ubiquitins to a protein is a universal disposal tag in cells: off to the proteosome, to be torn to bits. It gets stuck onto exposed lysine residues by the aforementioned ligase enzyme.

But less-thorough ubiquitination is part of other pathways. Other proteins can have ubiquitin recognition domains, so there are signaling events going on. Even poly-ubiquitin chains can be part of non-disposal processes - the usual oligomers are built up using a particular lysine residue on each ubiquitin in the chain, but there are other lysine possibilities, and these branch off into different functions. It's a mess, frankly, but it's an important mess, and it's been the subject of a lot of work over the years in both academia and industry.

The new paper has the crystal structure of thalidomide (and two of its analogs) bound to the ubiquitin ligase complex. It looks like they keep one set of protein-protein interactions from occurring while the ligase end of things is going after other transcription factors to tag them for degradation. Ubiquitination of various proteins could be either up- or downregulated by this route. Interestingly, the binding is indeed enantioselective, which suggests that the teratogenic effects may well be down to the (S) enantiomer, not that there's any way to test this in vivo (as mentioned above). But the effects of these compounds in myeloma appear to go through the cereblon pathway as well, so there's never going to be a thalidomide-like drug without reproductive tox. If you could take it a notch down the pathway and go for the relevant transcription factors instead, post-cereblon, you might have something, but selective targeting of transcription factors is a hard row to hoe.

Comments (9) + TrackBacks (0) | Category: Analytical Chemistry | Biological News | Cancer | Chemical News | Toxicology

July 17, 2014

TDP-43 and Alzheimer's

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Posted by Derek

There are quite a few headlines today about a link between Alzheimer's and a protein called TDP-43. This is interesting stuff, but like everything else in the neurodegeneration field, it's going to be tough to unravel what's going on. This latest work, just presented at a conference in Copenhagen, found (in a large post mortem brain study of people with diagnosed Alzheimer's pathology) that aberrant forms of the protein seem to be strongly correlated with shrinkage of the hippocampus and accompanying memory loss.

80% of the cohort with normal TDP-43 (but still showing Alzheimer's histology) had cognitive impairment at death, but 98% of the ones with TDP-43 mutations had such signs. That says several things: (A) it's possible to have classic Alzheimer's without mutated TDP-43, (B) it's possible to have classic Alzheimer's tissue pathology (up to a point, no doubt) without apparent cognitive impairment, and (C) it's apparently possible (although very unlikely) to have mutated TDP-43, show Alzheimer's pathology as well, and still not be diagnosed as cognitively impaired. Welcome to neurodegeneration. Correlations and trends are mostly what you get in that field, and you have to make of them what you can.

TDP-43, though, has already been implicated, for some years now, in ALS and several other syndromes, so it really does make sense that it would be involved. It may be that it's disproportionately a feature of more severe Alzheimer's cases, piling on to some other pathology. Its mechanism of action is not clear yet - as mentioned, it's a transcription factor, so it could be involved in stuff from anywhere and everywhere. It does show aggregation in the disease state, but that Cell paper linked to above makes the case that it's not the aggregates per se that are the problem, but the loss of function behind them (for example, there are increased amounts of the mutant protein out in the cytoplasm, rather than in the nucleus). What those lost functions are, though, remains to be discovered.

Comments (2) + TrackBacks (0) | Category: Alzheimer's Disease | Biological News

July 14, 2014

Modifying Red Blood Cells As Carriers

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Posted by Derek

What's the best carrier to take some sort of therapeutic agent into the bloodstream? That's often a tricky question to work out in animal models or in the clinic - there are a lot of possibilities. But what about using red blood cells themselves?

That idea has been in the works for a few years now, but there's a recent paper in PNAS reporting on more progress (here's a press release). Many drug discovery scientists will have encountered the occasional compound that partitions into erythrocytes all by itself (those are usually spotted by their oddly long half-lives after in vivo dosing, mimicking the effect of plasma protein binding). One of the early ways that people have attempted to try this deliberately was forcing a compound into the cells, but this tends to damage them and make them quite a bit less useful. A potentially more controllable method would be to modify the surfaces of the RBCs themselves to serve as drug carriers, but that's quite a bit more complex, too. Antibodies have been tried for this, but with mixed success.

That's what this latest paper addresses. The authors (the Lodish and Ploegh groups at Whitehead/MIT) introduce modified surface proteins (such as glycophorin A) that are substrates for Ploegh's sortase technology (two recent overview papers), which allows for a wide variety of labeling.

Experiments using modified fetal cells in irradiated mice gave animals that had up to 50% of their RBCs modified in this way. Sortase modification of these was about 85% effective, so plenty of label can be introduced. The labeling process doesn't appear to affect the viability of the cells very much as compared to wild-type - the cells were shown to circulate for weeks, which certainly breaks the records held by the other modified-RBC methods.

The team attached either biotin tags and specific antibodies to both mouse and human RBCs, which would appear to clear the way for a variety of very interesting experiments. (They also showed that simultaneous C- and N-terminal labeling is feasible, to put on two different tags at once). Here's the "coming attractions" section of the paper:

he approach presented here has many other possible applications; the wide variety of possible payloads, ranging from proteins and peptides to synthetic compounds and fluorescent probes, may serve as a guide. We have conjugated a single-domain antibody to the RBC surface with full retention of binding specificity, thus enabling the modified RBCs to be targeted to a specific cell type. We envision that sortase-engineered cells could be combined with established protocols of small-molecule encapsulation. In this scenario, engineered RBCs loaded with a therapeutic agent in the cytosol and modified on the surface with a cell type-specific recognition module could be used to deliver payloads to a precise tissue or location in the body. We also have demonstrated the attachment of two different functional probes to the surface of RBCs, exploiting the subtly different recognition specificities of two distinct sortases. Therefore it should be possible to attach both a therapeutic moiety and a targeting module to the RBC surface and thus direct the engineered RBCs to tumors or other diseased cells. Conjugation of an imaging probe (i.e., a radioisotope), together with such a targeting moiety also could be used for diagnostic purposes.

This will be worth keeping an eye on, for sure, both as a new delivery method for small (and not-so-small) molecules, fof biologics, and for its application to all the immunological work going on now in oncology. This should keep everyone involved busy for some time to come!

Comments (7) + TrackBacks (0) | Category: Biological News | Chemical Biology | Pharmacokinetics

July 8, 2014

An Alzheimer's Blood Test? Not So Fast.

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Posted by Derek

There all all sorts of headlines today about how there's going to be a simple blood test for Alzheimer's soon. Don't believe them.

This all comes from a recent publication in the journal Alzheimer's and Dementia, from a team at King's College (London) and the company Proteome Sciences. It's a perfectly good paper, and it does what you'd think: they quantified a set of proteins in a cohort of potential Alzheimer's patients and checked to see if any of them were associated with progression of the disease. From 26 initial protein candidates (all of them previously implicated in Alzheimer's), they found that a panel of ten seemed to give a prediction that was about 87% accurate.

That figure was enough for a lot of major news outlets, who have run with headlines like "Blood test breakthrough" and "Blood test can predict Alzheimer's". Better ones said something more like "Closer to blood test" or "Progress towards blood test", but that's not so exciting and clickable, is it? This paper may well represent progress towards a blood test, but as its own authors, to their credit, are at pains to say, a lot more work needs to