I definitely need to cover this recent work from Merck, because (1) it’s very interesting scientifically and (2) it has over 130 authors on the paper (!) It details the industrial synthesis of enlicitide, which is a beast of a macrocyclic peptide (see below!) Just looking at the structure tells you that this must be a ferociously active molecule with huge commercial potential, because there is just no way that anyone is going to make this on scale - or find a way to make this on scale! - otherwise.

This drug hits the PCSK9 pathway, which has been quite a story over the years. This target was famously discovered by finding a few people with mutations in the underlying gene who had bizarrely low LDL concentrations and who seemed to have correspondingly robust cardiac health. The first drugs on the market to take action on this idea were antibodies to block the receptor, and those were approved by the FDA some years ago as injectables.

They do indeed lower LDL, but (as that last blog post link notes) the results in humans have to be characterized as “good but not revolutionary”. I don’t know of any studies that show a definite advantage compared to statin (HMG-CoA reductase inhibitor) therapy, for example, although there are statin side effects in some patients that have to be taken into account. (On the other side of the question, statins seem to have some beneficial pleiotropic effects that we don’t quite understand, and whether these are shared by PCSK9 inhibition, I don’t know). And there are other people for whom statin therapy just comes up short, to be sure.

Several companies have tried over the years to come up with a small-molecule (well, smallish-molecule) approach that could lead to an orally dosed therapy as opposed to an injectable, and Merck has apparently made it over the finish line with this one. Here are the results of a trial in over 1900 patients (compared to over 900 in the placebo group) treated with the drug over a year, 20mg once a day. Over that time, the placebo group’s LDL went up about 3%, while the treatment group’s went down about 57%, which is what we call “pretty darn significant”, statistically speaking, with no differences in adverse events.

So now that you have a new cardiovascular drug, how do you make it for the hoped-for large patient population when it looks like, well, that thing to the right? That’s quite the multicyclic peptide, and while a lot of the key bond formations are good ol’ amide couplings, you have several that are not. The team divided up the molecules into “Western”, “Eastern”, and “Northern” pieces (based on the three macrocycles in the final structure) and demonstrated that they could make all of these in crystalline form (thus obviating the need for chromatographic purification). The Northern one was the toughest by far, with three unnatural amino acids and a choice of amine nucleophiles.

The answer to putting all this together was harnessing amino acid ligase enzymes, which lets you couple unprotected amino acid partners when everything is working right. The Merck team looked over a list of AAL enzymes and found one from Bifidobacterium adolescentis that was accomodating enough to deal with their intermediate. All of the candidates turned out to be able to handle peptide chains as the nucleophilic partner while only accepting single amino acids as the electrophile. That’s too bad in a way, because you could imagine assembling larger fragments this way, but if you get the enzymatic process running smoothly enough you can just turn things through it several times in a row. And without having to do protection/deprotection steps!

What looks like the nastiest traffic jam in the synthesis was the final stage of making that fragment, because you’re presented simultaneously with three amines and two carboxyls that need to be brought together in the proper pairings. The Merck group turned to esterase enzymes rather than proteases/amidases, not least because those can’t be tempted to run the amide formation in reverse because they don’t have the nucleophilic horsepower in their active sites. A previously-unreported enzyme from a Roseibacillus species showed promise, although I would certainly like to hear how many others got screened along the way, and even that one needed some engineering to increase its selectivity. They ended up being able to make the Northern piece with four enzymes and three separate building blocks in a single pot, which really is a tour de force.

To elaborate on to the final macrocycle the team called on thioesterase enzymes, which are generally what come into play in biosynthesis pathways for natural products of this type. Another (no doubt wide-ranging) screen identified a likely one from Brevibacillus laterosporus, but this also needed artisinal modification in its sequence to get the yields and selectivity up. I am skipping over a lot of work when I write sentences like that one!

The Northern and Eastern fragments also needed a reductive amination to bring them together, and a ketoreductase enzyme from a Kyrpidia species coupled with an imine reductase (from Pseudogymnoascus species) was used to make the requisite aldehyde, both after still more screening and protein engineering. This reaction mixture needed recycling of NADP/NADPH to run the synthesis enzymes, and still more enzymes were brought in for that cycle. In the end, the team achieved a one-pot five-enzyme process that did the overall transformation in 69% isolated yield.

Coupling this to the Western fragment was done through good ol’ chemical means (diphenylphosphinic chloride) while protected a stray primary amine that needed to be ready for the final macrocyclization. There are many such syntheses that have come to grief at such final steps; these macro-ring closures do not always want to happen easily. Another engineered thioesterase (this time from a Streptomyces species) was found to do the job and without the traditional need for high dilution. You often have to do that dilution to encourage your molecule to bite its own tail and make the large ring as opposed to reacting with another one nearby (which makes useless dimers or oligomers), so this enzymatic route is a huge help. The transformation comes though in 84% yield and >99% purity after liquid-liquid extraction and salt formation!

The overall yield, starting from 5-fluoro-N-aminohexyl tryptophan (you can see it hiding in there) is 39% and this has been run on multikilo scale with no chromatography. This is tremendously impressive, truly state-of-the-art process chemistry. I think we’re going to be seeing the reverberations of this work in macrocycle synthesis (and especially macrocyclic peptides) for a long time to come. Now to see if the drug itself performs up to its commercial and medical potential!

Coco is on the left.  I get her and Lizzie mixed up!  Two little black Pekes sitting together. 
No matter where their mom and dad are, they are watching.  And mom is being watched the most.  
Like here.  Coco is with her brother, Elwood, and he's joined them.  Their mom just walked out of the room.  Don't worry guys.  She's coming right back.  

We have quite a regulatory situation developing around a drug called avacopan (Tavneos), which is given to patients with a particular type of vaculitis. That’s a complex disease area, and comes in several varieties, but a common theme in many of them is an autoimmune attack against various proteins found in neutrophils. The drug is an antagonist of the complement 5a receptor in the innate immune system, and it’s given along with other immunosuppressants. 

It was developed recently by a company called ChemoCentryx, who ran a pivotal trial in 330 patients. Half got the standard of care plus a placebo and half got that standard plus the drug over 52 weeks, and the endpoints were remission at 26 and 52 weeks. Both endpoints were similar, and both showed a real benefit to the patients. Tavneos was approved by both the FDA and the European CHMP in 2022, and Amgen went on to purchase the entire company.

But earlier this year, the CHMP announced that they were starting an investigation based on reports of loss of data integrity in that trial. And the CDER at the FDA is proposing to have it withdrawn from the US market over the same issues. It’s very, very bad - here’s the FDA statement:

. . .new information that only became known to CDER more than three years after approval shows that unblinded study personnel manipulated the results of the pivotal clinical study so the drug looked effective when the original analysis did not support that conclusion. The applicant also did not disclose the original analysis to FDA, in violation of FDA regulations. CDER can no longer conclude that there is, or has ever been, a valid demonstration that TAVNEOS is effective for its approved use.

Ohhh boy. This is about as bad an accusation as you can make about a clinical trial, i.e. “The unblinded data were ugly, so we hocused the numbers until it looked like the drug worked”. I occasionally meet uninformed cynics who assume that this is how we always do things in the drug industry, but oh no, we don’t. We have an 85% failure rate in the clinic! Why would any clinical trial ever fail if we had constant recourse to bullshit like this?

For more details, this FDA document at the Federal Register is the place to go. This all came to light due to a lawsuit against the company for securities fraud, which included a consultant’s report about the avacopan/Tavneos trial process. That all came about because during the initial approval process ChemoCentryx made numerous public statement about how straightforward the trial was and how uneventful their interactions with the FDA had been, but in May of 2021 the FDA review committee hearing instead detailed a whole list of pointed questions the agency had had about the trial design and the interpretability of the results. That sent the stock down about 80%, and that will get you a shareholder lawsuit every time.

But as it turns out, the hapless shareholders don’t seem to have known the half of it. The consultant report introduced as evidence during the lawsuit claims that the initial analysis of the clinical trial showed it missing the primary endpoint, and that the company picked a number of cases for “readjudication”. Wouldntjaknowit, enough of these flipped over to positive during this reanalysis to cause the whole trial to meet its statistics. The report says that ChemoCentryx employees stated as much even before the reworking, calculating how many patient outcomes would need to be flipped. But none of this was disclosed in any way to the FDA, obviously, and yes, that is all flagrantly illegal if it’s what happened. 

The FDA says that it requested a detailed account of the data handling for the trial, and that Amgen’s response a month later “confirmed the key factual allegations” above. But the company went on to claim that the data in the NDA are accurate and that the patient readjudications were appropriate. (As it turns out, the lawsuit was later dismissed without ever addressing these accusations, so it doesn’t have any bearing on this situation).

The case for the data changes being valid rests largely on patient glucocorticoid dosing or missing data, and I won’t get into the merits of that argument. But what seems beyond doubt is that ChemoCentryx made sure that the FDA never heard about it and made sure to submit only the freshly polished data set. Such readjudication-after-unblinding was, as you would imagine, absolutely not permitted under the study protocols. The FDA notes that one of the patients was initially marked down by ChemoCentryx as a non-responder due to missing data at week 26, but that same patient got helpfully moved to the “in remission” category after the unblinding. That’s precisely why you are not supposed to do that sort of thing.

There’s even more bad news: not only are there doubts about the efficacy, the safety profile is looking bad, too. The FDA has received numerous reports of liver toxicity, which was a concern even during approval (Tavneos already has a label warning to that effect). But since getting on the market there have been several fatalities, some of which involve the extremely-alarmingly-named “vanishing bile duct syndrome”, which I had never heard of until now. It’s just what it sounds like: the bile ducts through the liver tissue deteriorate and disappear, and that is clearly just as bad as you think it is. Most of those have been reported in Japan, for reasons unknown, but man, you don’t want that showing up anywhere. I feel pretty sure that a “Whatever happened to the bile ducts” finding during the trials would have shut things down right there. One has the impression that Amgen might have been better off if they'd never heard of this drug at all instead of being shackled to defending it.

The drug was approved with a requirement for a postmarketing study covering both safety and efficacy, but the FDA says that as of the most recent report, only 21 of the planned 300 patients had been enrolled. I’ve written about this problem before - too often, companies have an incentive to draaaaag their feet on these requirements and collect the data at glacial speed, and that may be just what we’re seeing here.

But as it stands, I would agree with the FDA’s contention that the trial results “are uninterpretable and cannot be salvaged with further analysis”. What’s more, it would seem that the company made materially false statements to the agency during the application process. This is all really, really unfortunate - for vasculitis patients most of all, but for the integrity of the whole clinical trial and drug approval process as well. We really don’t need this sort of thing right now - hell, we never have, but especially not now.

So let’s finally talk about peptides. And I don’t mean peptides as chemists and biologists understand them (short chains of amino acids) I mean “Peptides!”, the hot new wonder drugs that you can order by mail. Oh man.

The first barrier to writing about this situation, for someone like me, is that difference in terms. For a chemist, “peptide” has a pretty clear definition: any relatively short chain of amino acids, and when they get longer we go ahead and call them “proteins”, although the dividing line is a matter of personal opinion. So the number of different possible peptides is just ridiculously huge. If you just pick (say) a ten-amino-acid chain with the 20 common amino acids, that’s twenty to the tenth power, which is over ten trillion possibilities. For comparison, it has been about ten trillion seconds since Homo sapiens emerged as a separate species.

And since that number is large and contains multitudes, there are lots of physiologically active peptides and an even much more gigantic mass of them that biologically do nothing at all. As you digest any particular piece of protein (being from Arkansas, I recommend a plate of barbecue or fried catfish) the enzymes in your stomach and small intestine are producing huge numbers of progressively shorter peptide chains as they break down that food on the way to stuff that will be absorbed into the bloodstream. And this is while every living cell is making progressively longer peptide chains off the ribosomes, building back up the proteins needed for life. This is why I I had a puzzled look on my face when I first saw people talking excitedly about how they were taking “peptides” as if that were a well-defined category that everyone knew about.

Mentioning digestion brings up the question of stability. Your body is also awash with enzymes (proteins themselves!) that do a terrific job of breaking down peptide bonds. So the lifetime of any random protein string in the blood is probably going to be limited, but the subject of today’s post is not random peptides. Nope, it’s amazing wonder peptides ordered from suppliers who mail them directly to your house, stuff that will variously energize your waking hours, cure your diseases, melt your fat deposits, build your muscles, grow your hair, and extend your lifespan. You’re not going to be taking these things orally, because unless a really substantial amount of engineering has gone into it, any given peptide is going get the same treatment from your digestive system as a chicken breast does, i.e. a complete teardown. These mail-order peptides are injectable items.

At one point that would have severely limited their use, but the advent of the GLP-1 drugs (proteins as well, which are largely but not exclusively injectables) has made this more acceptable, at least among people who don’t know someone who has to inject insulin (which needless to say is a small protein itself). So the times have come around to make this a real business opportunity, which many suppliers are enthusiastically leaning into.

How about the science? It’s the biggest mixed bag you ever saw. There’s no doubt at all that there are some extremely biologically active peptides out there, and more such things are being discovered all the time. In fact, there’s a whole field devoted to looking at peptides that are too short to have been studied by the usual analyses, and those folks are turning up all sorts of activities that we never even appreciated were there. So that’s the first point: there are indeed a whole range of physical and medical effects to be found in these things.

Unfortunately, point two is that we barely have any of these effects worked out - at least not to the degree that you would want before you start injecting them into your leg. We’re still finding things out about extremely well known active proteins like insulin, much less more recent discoveries. That lack of knowledge extends - and how - both to their on-target effects (assuming that the target or targets are reasonably well known, which isn’t always the case) and to their off-target toxicities. 

And there are going to be plenty of cases where yes, Peptide X sure does do that thing you’re interested in, but it turns out that you can’t do That Thing without doing other things that you are surely not interested in. A number of “peptides of abuse” these days, for example, seem to be targeting human growth hormone pathways and associated ones, so let’s use that as an example. The pitch is often something like “Here’s the signal your body uses to build muscle! Take it directly and get going today!”, and with HGH there’s also been a longstanding subculture that treats it as a Fountain of Youth signal of some kind. “Replenish your growth hormone levels”, the idea is, “and dial back the biological clock!”

But growth hormone (and I shouldn’t have to say this) is powerful stuff, and it doesn’t just go tell your muscles to swell up. It affects bone tissue and many other tissues as well. I would invite anyone looking to maximize their growth hormone levels to look up a condition called acromegaly, which is what you get when your body keeps on making more growth hormone than you strictly need. Bones in the hands, feet, and head enlarge, and you get all sorts of side effects like joint pain, high blood pressure, type II diabetes, and other things that are probably not mentioned in the peptide supplier’s brochure. 

Excess growth hormone also increases the risk of some types of cancer, and that is a general problem with any attempt to (re)activate cellular growth pathways. Cancer, when you get right down to it, is a disease of unrestrained cellular growth, and there are a lot of different pathways that can lead to it. Stimulating cell growth out of the blue with systemic injections of synthetic hormone-like peptides is (in my view, and it ain’t just me) an invitation to greater tumor risk. And that’s just for starters. 

There are two very good pieces over at Stat right now on this topic. One, by physician Vikas Patel, describes a patient who is discontinuing her statin therapy - very inadvisably, given the clinical presentation described - but is enthusiastic about “BPC-157” as an injectable peptide for her knee pain. Says Patel:

My patient is refusing a drug studied in 170,000 people because of side effects that a 124,000-person analysis just confirmed do not exist — while injecting a compound studied in 14 humans, from unregulated sources, based on the recommendation of someone who profits from selling it. She’s probably not the only one. And those using it believe they are “doing their own research.”

The other one (by Sarah Hood) relates all this to RFJ Jr.’s advocacy. The flip side of “the government shouldn’t be able to force me to vaccinate my kids” is “I should have the right to take whatever medicines I want to without the government getting in my way”. That’s what we’re seeing here. I would bet that many peptide customers see themselves as free agents who have done their own research and are taking their health into their own hands - and dodging past Big Med and the old fossils at the regulatory agencies while they’re at it. But as that article points out (and as I’m doing today), what they’re actually doing is rolling the dice after falling for sales pitches aimed at exactly this sort of customer.

That dice rolling doesn’t just end at the unknown mechanisms of action, the lack of human data, and the lack of information about potential side effects. You’re also ordered from suppliers whose manufacturing standards you are in no position whatsoever to check, no matter how much of a free health warrior you might be. You don’t have an LC/MS or an NMR machine in your garage, so you can’t be sure what it is you’re really injecting, how pure it is, or to what extent it’s already deteriorated on standing. There is no one at the other end of the deal who cares very much, either, believe me. Human nature being what it is in this fallen world, you actually need regulatory agencies to force people to care about these issues by threatening them with severe punishments if they don’t.

In my own view (and it ain’t just me) you also have regulatory agencies to force people to show that their drugs actually have some benefit before they can sell them, too. But that’s going further and further out of fashion. Can’t get ahold of the New Hotness to inject into your upper thigh if there are a bunch of stick-in-the-mud folks asking for human data, infringing on your freedom and all. What a time to be alive.

This weekend brought news that the Russian opposition leader Alexei Navalny was poisoned in prison by the compound epibatidine. That is not (to put it delicately) the first thing one would have expected, so I wanted to give a little background on this compound first.

It’s a toxin isolated from a frog species found in Ecuador and Peru (and a few of its relatives), and like all poison frogs it is a very festive-looking creature indeed. That is of course a warning to potential predators, as with many brightly colored species around the world, a little evolutionary message to any hungry onlooker that they can afford to be so bright and prominent for a very good reason that you should have had a chance to learn by now. Many such frogs are used by native groups in the New World jungles as arrow-poison sources, although this particular species doesn’t seem to be.

It has a simple structure with one rather unusual feature, that 2-chloropyridine group. You do see halogenated natural products, but more often from marine organisms where chlorine and bromine are more easily available. An even weirder-looking related alkaloid with the same group in it (phantasmidine) is also found at lower concentrations in the frogs. Unfortunately, the biosynthesis of these compounds has not yet really been worked out (to my knowledge). It is known, as with most other poison dart frogs, that if you raise them in captivity they do not produce the toxin: there is something in their natural diet or environment that allows for it that is not found under terrarium conditions. Even under jungle conditions, sometimes one population of frogs will have the toxin while another in a different location does not.

It is very likely that the frogs do not have the ability to produce the compound on their own, but instead acquire it from their diet of local insects, etc. and then sequester the epibatidine in their skin. This has been documented with both birds and frogs with another such case, batrachotoxin - that one is chemically distinct from epibatidine and is found in a different genus of frogs, but it’s likely a similar underlying story. Not knowing the exact species that produce these compounds has made studying the chemical pathways behind them rather difficult!

And as with all such compounds, an immediate question is how the creatures that produce or sequester them manage to avoid poisoning themselves. Edit: here's how they do it, apparently, by co-evolving a mutant form of the receptor. This does not come without a cost, it seems. Another paper reports that this Epibatidine works as a ligand for both the muscarinic and nicotinic receptors - it’s an agonist, substituting for the natural ligand acetylcholine, and in general messing with the cholinergic system is going to lead to some strong effects. If you strongly block such signaling, you have replicated the mode of action of nerve gas, and if you strongly enhance it (as in this case) you can get a range of effects including analgesia and muscle paralysis. That latter one is especially unwelcome in the respiratory and cardiovascular system, clearly, and there is no antidote. The compound’s pharmacologic window between interesting pain relief qualities and seizures-n’-death is unfortunately quite narrow. 

People have tried to widen it, most notably Abbott (AbbVie) in the 1990s. They did a lot of work in this area looking for a nonopioid pain compound and took a chemical cousin of epibatidine (ABT-594, tebanicline) into human trials. They had definitely gotten rid of the “death” side effect by that point, as the FDA tends to insist on, but the window between analgesia and the remaining side effects was still too small. These included nausea, vomiting, impaired coordination, and apparently rather weird dreams as well. People were dropping out of the treatment group in the Phase II with alarming frequency, and the compound was abandoned. There are still a number of possible opportunities in the selective-nicotinergic-agonist area, but realizing selective cholinergic agonists is a problem that stretches back many decades and no general solutions have been found.

OK, back to the present day. The presence of the compound in Navalny’s body seems to be beyond dispute. He died two years ago in a “special regime” prison in Siberia, and his body was returned to his mother. Numerous toxicological examinations have confirmed the epibatidine, which does not undergo much metabolism in the human body. That along with its unusual structure make it very easy to identify. I am in agreement with those who believe that this was a deliberate choice by Vladimir Putin’s regime. After all, they had tried to kill Navalny in 2020 with what was obviously a Russian-manufactured nerve agent, and that was after previous chemical attacks in 2017 and 2019. The use of a tropical frog poison in Siberia is to me a grim joke and a statement that this was obviously an unnatural death that was carried out by people with obvious knowledge of human poisons. You don’t need the frogs: epibatidine itself is not that hard to synthesize in the lab by a variety of published routes. It can be made in quantity by any competent organic chemist who knows enough to take the proper precautions, and Russia as a country has a great many skilled organic chemists.

The Russian military and security services have been experts in poisoning people with exotic materials for a long, long time. They know exactly what they are doing from a chemical point of view, even if some of their assassins have not been particularly competent or well-informed themselves. Some have speculated that the authorities wanted to try out the epibatidine route to see how well it worked, but let’s be realistic: they could have done that on all sorts of other Siberian prison inmates without anyone ever hearing about it. I don’t think that the Russian state services have many review-board problems when it comes to running human trials. 

No, this was murder, obvious murder, and it was set up to be an obvious murder. Vladimir Putin is a corrupt, lawless poisoner, and he has had no qualms about demonstrating this over and over. He’ll order it done again the next time the opportunity presents itself.

Here’s an oddity that I’m glad was put to the test of a controlled trial. It seems that retrospective studies on cancer immunotherapy patients had suggested that there might be an advantage to giving the infusions earlier in the day, so this team took 210 non-small-cell lung cancer patients and divided them into two groups. One got the infustion early in the day (from 7:30 AM to 2 PM), and the other later (from 3 PM to 8 PM). Some of the patients were taking sintilimab and others pembrolizumab. 

The results are surprisingly strong: the early-infusion group had a median progression-free survival (PFS) of 11.3 months, while the late-infusion group’s median PFS was 5.7 months. Overall survival was median 28 months and 16.8 months for the two groups, and both results were (as they sound!) highly statistically significant. I’d be willing to bet that even the organizers of this trial weren’t expecting readouts this definitive. Subgroup analysis showed that this held for people taking either of the immunotherapy drugs mentioned. 

So what’s going on here? Some circadian-rhythm explanation seems inevitable here. The team found that the early-infusion group had increased levels of T cells (and increased levels of activated ones, on top of that), but the connection is between that and diurnal timing is still unclear. That is going to be a very interesting thing to figure out. I am certainly willing to believe nearly anything about the immune system at this point! The first step will be to replicate this effect, of course, and it’s an easy enough intervention that I hope that we see this happening soon.