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Finding satoshimycin

As part of fundraising using bitcoin, I promised that if I raised more than 10 BTC (I got a bit more than 11 BTC total), I’d start testing other molecules in the 9DS family, one of which would be named “Satoshimycin”. Why do we want more compounds? Drug discovery is a bit of a gamble. Sometimes, drug candidates can fail in the late stage due to something you couldn’t have predicted from first principles. It would be silly to discount the 9DS family of compounds and, broadly speaking, the medicinal strategy, based on the success or failure of a single example. Given that drug discovery is an expensive process, one of the most effective ways for indysci to promote open-source pharmaceuticals is to shepherd multiple candidates through early stages, especially since within the 9DS family, the infrastructure and strategies are shared.

Luckily, this is a relatively easy process; the way 9DS is made is by feeding a molecule to the soil bacteria that produce sibiromycin. The bacteria integrate this compound by substituting it in the sibiromycin structure, effectively deleting the section that causes cardiotoxicity. If we feed a slightly modified compound instead, the homologous modification should be incorporated into 9DS.

Of course, that’s in theory. In practice, subtle chemical effects, like the fed compound bumping into the walls of an enzyme, or a structural modification changing the reactivity of a distant part of the molecule, can result in a failure to incorporate the modified compound. There are, broadly speaking, five ways this experiment can fail:

The fed compound is toxic to the soil bacteria. This could kill them completely or, more frustratingly, weaken them so that the culture is more vulnerable to contamination by fungus or other bacteria. The new compound doesn’t get made by the soil bacteria. Some of the reasons for that are covered above. Another possibility is that the fed compound is too insoluble in water to be present in appreciable quantities to engage the production enzyme. The new compound is made by the soil bacteria but it kills the soil bacteria before they can pump it out of their system. The 9DS family members are broad-spectrum DNA-jamming chemotherapies, and sibiromycin was initially discovered because it killed bacteria. So this is a real possibility. The new compound gets made, and is produced, but it fails to get into the test bacteria. One possible way to get around this is by testing it against a different type of test bacteria, although I doubt the modifications are significant enough that this failure mode is a possibility. The new compound gets made, and is produced, and it gets into the test bacteria, but it doesn’t jam the DNA and has no effect. There might be something special about bacterial DNA, versus cancer DNA, but my gut feeling is that for the most part DNA is DNA, and if it has no effect due to this reason it’s not worth pursuing further.

The first positive result that has cleared all of these hurdles, is in. On the left is a picture of the bacterial plate that was used to test the culture growing satoshimycin. You can see a zone of clearance around well #1 where I deposited media which should have had bacteria producing 8-MeO-DHS. #3-6 were 9DS-producing controls, although culture #6 appears to have failed (and indeed that culture smells funny). In well #2, I tried a different variant, 8-CF 3 -DHS.

It’s very encouraging that the clearance is about as much as the clearance for 9DS, which means that the potency of the compound will be similar. I’m also not entirely surprised that this particular variant was the first to really make it. Structures 8-MeO part of the molecule is found in other compounds, such as SJG-136, which is a drug in phase III trials.

Describing satoshimycin using a (non-systematic) name

Assigning a descriptive name to describe satoshimycin can come from several directions. One is to start from 9-deoxysibiromycin and notice that there’s an extra oxygen atom at position 8. This leads to the clunky name 8-oxo-9-deoxysibiromycin. There is a related compound called ‘sibanomicin’ (that’s with an i instead of a y), which kind of looks like 9DS. One difference is that the ring on the “northwest” side is bare. The other difference is the tail on the “east” side has more hydrogens – five instead of three. The molecule less two hydrogens is “dehydrosibanomicin”, and adding the methoxy makes it 8-methoxy dehyrosibanomicin, or 8-MeO-DHS. Incidentally, 9DS could also be 8-Me-DHS, but 9DS is simpler.

Why -mycin versus -micin? Compounds with the suffix -mycin or -micin come from a family of soil bacteria called actinomyces. -Mycin compounds come from the subfamily streptomyces; -micin compounds come from the micromonospora subfamily. Incidentally, sibiromycin and 9DS come from neither, but from a third subfamily called streptosporangia, but the bacterial family tree has been revised since its discovery. These soil bacteria are closely related and in the environment, and the gene to make chemicals get passed around, so it shouldn’t be surprising that distinct species from two subfamilies happen both make similar compounds. Because we’re using the streptosporangium strain to make 9DS and satoshimycin, I’ll stick to the -mycin suffix for the new name, and -micin for the descriptive name.

What’s next for satoshimycin?

After I’ve accumulated enough 9DS to finish the primary objective of Project Marilyn (testing in a mouse xenograft study), I will shift production over to satoshimycin, and prepare enough to take an NMR, and probably a mass spec, of the structure. This will confirm that I’ve made what I think satsohimycin is. If I discover other compounds in the family, I’ll roll all of them together in a publication-quality account, post to BioRxiv open-access preprint server, and then start shopping around for a peer-reviewed journal to host it.

More compounds?

So far I’ve tested what should have made 8-Cl-DHS, 8-F-DHS, 8-MeO-DHS, and 8-CF 3 -DHS. If you look at the pictured plate, there’s vaguely a bit of clearance around 8-CF 3 -DHS, and I haven’t tested 6-Me-DHS yet. The other two have failed, but it could also be because the bacteria aren’t “trained” to make these compounds. It took several months of growing and selecting ‘best batches’ to successfully produce 9DS, and it may yet require that for the other compounds. I’m not ready to give up on them yet, the work will continue. We need more open-source drug candidates.

Donating bitcoin

If you’d like to donate bitcoin to further research Satoshimycin and other drug candidates, you can do so at:

1GPR5GZHffW77myt9WbA5ot3fDHkzKSQTo

or scan this QR code with a mobile bitcoin app:

A shout out to the folks at Airbitz who made this round of accepting bitcoin donations easy.