Jennifer Clark

Isomerization-based strategies to enable the stereodivergent construction of complex polyenes from geometrically defined alkene linchpins remain conspicuously underdeveloped. Mitigating the thermodynamic constraints inherent to isomerization is further frustrated by the considerations of atom efficiency in idealized low–molecular weight precursors. In this work, we report a general ambiphilic C₃ scaffold that can be isomerized and bidirectionally extended. Predicated on highly efficient triplet energy transfer, the selective isomerization of β-borylacrylates is contingent on the participation of the boron p orbital in the substrate chromophore. Rotation of the C(sp²)–B bond by 90° in the product renders re-excitation inefficient and endows directionality. This subtle stereoelectronic gating mechanism enables the stereocontrolled syntheses of well-defined retinoic acid derivatives.

I wanted to note something today that won’t make many headlines outside of biopharma, but it’s just the sort of story that I wish more people knew about. Let’s start with this: there’s a terrible disease called IPF, idiopathic pulmonary fibrosis. Anyone with any medical background knows to beware the word “idiopathic”, since it’s a shorthand for “we don’t understand much of anything about this”. You’ll also know to beware the word “fibrosis”, for that matter, because it generally means a buildup of scar tissue that no one can do very much about. IPF happens in older patients, more males than females, and its features are progressive scarring of the lung tissue, driven by some ultimate cause that we haven’t quite been able to work out. The decline in lung function is progressive and irreversible, and most people who get the diagnosis are dead within a few years – short of a lung transplant, there’s really little to be done about the underlying problem. Pirfenidone and nintedanib are approved compounds for the disease, but in most cases they just slow down the inevitable a bit.

Now, this is part of a broader field of fibrosis diseases, affecting all sorts of organs and tissues (heart, lung, liver, kidney, etc.) Some of these we understand better than others, and we understand enough to know (simultaneously) that classifying so many things under “fibrosis” is an overreach, because such tissue effects are a symptom of something deeper (that “something” can be pretty wide-ranging), but also that the cell biology of fibrosis itself is often similar enough to make one hope for a relatively broad-based treatment of such symptoms. Which would definitely be an improvement over what we have now.

Back in 2012, Biogen bought a small company called Stromedix (founded in 2007) that had a candidate aimed at IPF. There’s a biotech-biz inside baseball angle to the story, because the founder of Stromedix was a former head of Biogen’s R&D (and has gone on to other ventures since), Stromedix came out of one of the well-known VC organizations here, Biogen had actualy developed the program initially, outlicensed it to Stromedix, and eventually came back around again, and so on. As with any technology hub, everybody either knows everybody or knows someone who knows them, and a lot of interesting stories get generated. But I’m leaving the human-interest and business angles aside, and focusing on the science and medicine.

The main compound involved, STX-100, is an antibody targeting the alpha-v-beta-6 integrin receptor. That’s upstream of TGF-beta, which has been shown to be a key player in fibrosis in general. (There’s one of those hopes for a general treatment). The integrin activates TGF-beta, so the hope was that targeting it would slow down or even halt the fibrosis process. Targeting TGF-beta directly is very likely a bad idea (it has just too many important functions), so there have been all sorts of attempts to bounce-shot the target by finding other targets that regulate its activity. The antibody had already been in trials for kidney fibrosis, but had shown some tox problems which apparently made it a better candidate for lung fibrosis – they’d gone into kidney patients first because there were easier to identify and monitor. And that’s where Biogen came back into the picture, buying the whole company and pushing the trials forward, because they’d looked at pulmonary fibrosis with it earlier and seen encouraging results.

STX-100 (now BG00011) went back into the clinic, with a trial ending in early 2017. But there wasn’t much news about that, although a Phase IIB went ahead in IPF patients last year. And (you probably knew where this was going), word has just come out that the study has been terminated with only about a third of its patients enrolled. That does look like the end of the line for this antibody, and it’s not particularly encouraging news for targeting alpha-v-beta-6 either (although there’s a small-molecule antagonist of it from GSK that’s in the clinic now (edit: now terminated as well). And there are, fortunately, many other mechanisms being investigated by many other people, with quite a few trials going. Fibrosis is a major unsolved problem, and the first people who make real progress against it will do very well, and help a lot of people who have, frankly, very little hope other than something new appearing from R&D.

And that’s what I wanted to highlight: here’s a big cause of human suffering that not many people are aware of outside the medical field. The first time most people become aware of fibrosis as a disease is after they or someone they know is diagnosed, and that isn’t good news at all. There are, though, a great many people in academia and industry who have been working on this from many different angles for a long time now, but if you’re not a biomedical researcher you will never have heard about any of that work at all. I would also add that a tremendous amount of time, effort, and money has gone into all this, by the time you add it all up, and so far (from a can-you-help-me-doctor perspective), there’s been little to show for it. We’ve gained a lot of knowledge and experience, and (as this latest news shows) closed off some ideas previously thought promising, but there is no fibrosis cure to announce. Yet.

You will not see any big headlines about the demise of STX-100, either. Drugs fail all the time, most of the time rather quietly, and all the work and money that went into them just sort of vanishes. But that work, and that time, and that money – all of them were very real. As were the hopes of the people working on the drugs, and the hopes of the patients taking them in the clinical trials. This is happening constantly in the background, all the time, and it’s one of the big reasons that I started this blog in the first place, because almost no one realizes it.

Well, people have been searching for a reaction like this one for quite a while now: that link describes a catalytic Mitsunobu-like reaction, and the original has always been a transformation that synthetic organic chemists groan about but use anyway. It’s a way of substituting an OH group in one pot with what should be clean stereochemical inversion, and you can use a variety of nucleophiles. One common use is inverting a stereocenter by forming an ester product – hydrolyze it and you’ve got the alcohol back in the opposite stereochemistry. And it’s also used a lot to make ethers, particularly for intramolecular ring-forming ones or acyclic aryl ether formation. It’s been around for decades, it’s all over the literature, and you’d have to search for a bit to find a working synthetic chemist who’s never run one. So why all the grumbling?

Because it’s a mess. The classic Mitsunobu uses stoichiometric diethylazodicarboxylate and stoichiometric triphenylphophine, and the latter ends up as triphenylphosphine oxide. That last conversion is the thermodynamic “battery” that runs a number of organic chemistry transformations (such as the original Wittig reaction), but no one is happy about dealing with all the phosphine oxide when it’s purification time. Sometimes you can extract your product out or precipitate the TPPO out and get away clean, but other times it’s a slog. And you never feel like you’re doing elegant chemistry when you chew up so much reagent (both the DEAD and the TPP) to do something like flip a single OH group. If “atom efficiency” is your thing, you have to avert your eyes from the Mitsunobu.

I would not like to count the variations that have been proposed over the years, but most of these have involved alternatives to the azo reagent and still produce a phosphine oxide. Polymer-supported reagents, more water-soluble variants, all sorts of things have appeared. But getting both catalytic has been a tall order, because the DEAD gets reduced in the reaction while the TPP gets oxidized, so you’re going in two directions at once if you want to cycle those around. This new paper, though, has an ingenious solution shown at right. You start with the phosphorus already in the +5 oxidation state and go through a reactive cyclic intermediate that gets regenerated. So the reaction is catalytic in both directions (the oxidation and the reduction) and throws off only an equivalent of water as a byproduct. Pretty slick!

This also lets you do esterification on alcohols that are sensitive to the more common methods, and the pre-oxidized phosphine lets you get away with substrates that have groups (alkyl bromides/iodides, azides) that would reaction with triphenylphosphine itself. The authors (Univ. of Nottingham and GSK) do a thorough mechanistic investigation into the reaction, and they note that this system might also be applied to other phosphine/phosphine oxide driven reactions.

If this works as well as advertised – and I see no reason up front to think it doesn’t – then I would expect this to almost entirely replace the original Mitsunobu, which has had an over fifty-year run as a synthetic chemistry workhorse. It will also kill off the market for DEAD and similar reagents; if there were a good single-supplier play for azodicarboxylates I would have gone short their stock immediately on reading this paper. Congratulations to the authors!

Nucleophilic substitution reactions of alcohols are among the most fundamental and strategically important transformations in organic chemistry. For over half a century, these reactions have been achieved by using stoichiometric, and often hazardous, reagents to activate the otherwise unreactive alcohols. Here, we demonstrate that a specially designed phosphine oxide promotes nucleophilic substitution reactions of primary and secondary alcohols in a redox-neutral catalysis manifold that produces water as the sole by-product. The scope of the catalytic coupling process encompasses a range of acidic pronucleophiles that allow stereospecific construction of carbon-oxygen and carbon-nitrogen bonds.

This Review summarizes the advances in fluorination via C(sp2)–H and C(sp3)–H activation. Transition metal catalyzed approaches championed by palladium have allowed the installation of a fluorine substituent at C(sp2) and C(sp3) sites exploiting the reactivity of high oxidation transition metal fluoride complexes combined with the use of directing group (some transient) to control regio‐ and stereoselectivity. The large majority of known methods employ electrophilic fluorination reagents, but methods combining a nucleophilic fluoride source with an oxidant have appeared. A number of ligands have proven to be effective for C(sp3)–H fluorination directed by weakly coordinating auxiliaries, thereby enabling control over reactivity and selectivity. Methods relying on the formation of radical intermediates are complementary to transition metal catalyzed processes as they allow for undirected C(sp3)–H fluorination. To date, radical C–H fluorinations mainly employ electrophilic N–F fluorination reagents but a unique bio‐inspired Mn(III)‐catalyzed oxidative C–H fluorination has been developed. Overall, the field of late stage nucleophilic C–H fluorination has progressed much more slowly, a state of play explaining why C–H 18F‐fluorination is still in its infancy.

Autotaxin (ATX) is a secreted glycoprotein and the only member of the ectonucleotide pyrophosphatase/phosphodiesterase family that converts lysophosphatidylcholine (LPC) into lysophosphatidic acid (LPA). LPA controls key responses, such as cell migration, proliferation, and survival, implicating ATX–LPA signaling in various (patho)physiological processes and establishing it as a drug target. ATX structural and functional studies have revealed an orthosteric and an allosteric site, called the “pocket” and the “tunnel,” respectively. However, the mechanisms in allosteric modulation of ATX's activity as a lysophospholipase D are unclear. Here, using the physiological LPC substrate, a new fluorescent substrate, and diverse ATX inhibitors, we revisited the kinetics and allosteric regulation of the ATX catalytic cycle, dissecting the different steps and pathways leading to LPC hydrolysis. We found that ATX activity is stimulated by LPA and that LPA activates ATX lysophospholipase D activity by binding to the ATX tunnel. A consolidation of all experimental kinetics data yielded a comprehensive catalytic model supported by molecular modeling simulations and suggested a positive feedback mechanism that is regulated by the abundance of the LPA products activating hydrolysis of different LPC species. Our results complement and extend the current understanding of ATX hydrolysis in light of the allosteric regulation by ATX-produced LPA species and have implications for the design and application of both orthosteric and allosteric ATX inhibitors.

Scalable total synthesis and comprehensive structure–activity relationship studies of the phytotoxin coronatine

Scalable total synthesis and comprehensive structure–activity relationship studies of the phytotoxin coronatine, Published online: 16 March 2018; doi:10.1038/s41467-018-03443-1

Development of comprehensive structure–activity relationships for coronatine has been a major goal in the agrochemical industry. Here, the authors report the gram-scale production and structure–activity relationship of parent coronafacic acid and ultimately rationalise the biological activity of analogues of this phytotoxin.

Abstract

I only have time for a short post this morning, but here’s a technique that I had never thought about: palladium-catalyzed drug synthesis inside the target cells. There have been a few reports of activation of prodrugs via intracellular Pd catalysis (such as this one), but it seems like a real challenge to get both components and a bio-compatible Pd catalyst into the cell at the same time and place. The earliest report in this field that I know of is from the same Edinburgh group that’s reporting this new work.

They’ve produced Pd-loaded microspheres and conjugated those to cRGD, a tumor-targeting peptide (via integrin receptors) that increases cellular uptake of the microspheres. (It’s been used for similar purposes for many other drugs and nanotech species, as those who follow that literature will know). The catalyst was internalized quite readily in the cell lines of interest, and was decreased by the appropriate competition experiments, so the first step worked as planned.

A test with a Pd-catalyzed deprotection to give a fluorescent species also worked, so the next step was to try the two reactions shown at right: deprotection of 5-fluorouracil and coupling to produce the kinase inhibitor PP-121. These reactions both took place under buffer conditions, and in the presences of  U87-MG, none of the precursors showed cytotoxicity on their own, alone or in combination (nor did the Pd microspheres). In the key experiment, the cells were exposed to the Pd-loaded microspheres, washed to remove any extracellular Pd, and then exposed to the compounds of interest. As you can see in the figure, cell viability did indeed decrease, and it decreased even more when the cells were exposed to both sets of precursors at once (as well they might).

I would still wonder if any Pd leached out into the surrounding media, though, especially as some cells began to die off, and whether some of the cytotoxic compounds were formed extracelluarly. The fluorescent experiment, though did indicate that the Pd reactions can and do take place in the appropriate cell compartments, so it’s reasonable to assume that this is happening with the drug cases as well. A further test of this technique might involve producing a therapeutic compound that is known to have such poor cell penetration that it’s inactive in such assays, but which could be broken down into cell-penetrant precursors. I have no candidate in mind, off the top of my head, but it would be a dramatic demonstration, and also point to a practical use of the technique.