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Analytical Chemistry

Sticking Together in Solution

I will cause no controversy by saying that most of the small-molecule compounds that we develop as potential drugs in this business are rather poorly soluble in water. Every organization I’ve worked in has made the standard jokes about “brick dust” and “powdered Teflon”, and for the well-founded standard reasons. A lot of binding sites in proteins tend to be more hydrophobic than the surrounding solution – that’s one of the ways that you get the thermodynamics of compound binding to work, of course, because if everything were joyously happy out there in solution by comparison, why would they bind at all?

There are, of course, really polar binding sites, and those bring in specifically arranged salt bridges (lots of lysines and arginines, if you’re binding something like a phosphoylated species, or lots of glutamate and aspartate if the protein is going the opposite way), but even those have their hydrophobic spots in them. Those polar interactions tend to be a lot snootier in their distance and angle preferences than grease-recognizes-grease, though, so targeting them is generally a lot trickier. It’s easy to miss the preferred orientation, and if you try to stick a really polar/charged part of your molecule into a binding-site region that isn’t recognizing it, the result is generally far worse than neutral. The polar upside is harder to attain while the downside is easier, so medicinal chemists thus tend to rely on hydrophobicity as the default position, with polar functional groups judiciously sprinkled in. That also matches up well with our chemical abilities, as fate would have it. We tend to work best in organic solvents, because there’s a wider variety of bond-forming reactions available under nonaqueous conditions, and purification of the products is more straightforward.

All of that is by way of apology to our colleagues in the formulations labs, who have to deal with the results. It’s often not pretty. Many well-known drugs have pretty hideous aqueous solubilities, and the recent trend towards even larger molecules than usual (protein-protein interaction inhibitors, bifunctional degraders, and so on) is not helping much, either. The list of tricks to mitigate the problem is a long one, and unfortunately it’s pretty darn empirical as well, since the kinetics and thermodynamics of getting into solution (and staying there) can be very complex. There are, for example, compounds that seem pretty freely soluble at first, but will find ways to crash back out if you leave them around for a while (often by forming less-soluble aggregates), and there are others that have pretty decent solubility but take their sweet time to realize it, and everything in between.

This recent paper will give you some idea of the fun that is in store. It’s looking at one of the ways that you can get poorly soluble molecules in at higher concentration, through the addition of “hydrotopes”. Those are added molecular species that somehow stabilize other ones in water. It’s known that these generally work by piling up around the less-soluble molecules and acting as a sort of bridge between them and the bulk watery phase, but you’ll note the hand-waviness of that explanation. Knowing what’s going on in more detail would be of great use in picking likely candidates and designing new ones.

The paper linked to (from Hebrew Univ. in Jerusalem) is studying good old caffeine, which despite its ubiquity in coffee, tea, and soft drinks is actually not all that water-soluble. It has a tendency to form oligomers and aggregates in water, like many drug substances will, and that can give you a range of behavior: outright precipitation, sure, but also still-in-solution-but-less-efficacious, which is quite annoying. There are a range of hydrotopes known to affect caffeine’s solubility, things like urea and thiocyanate which act in many such situations, but they affect the single molecules and the oligomers in the same way.

This work shows an interesting effect of sugar molecules, though: as others had noted, the addition of such species decreases the general solubility of caffeine, but on closer inspection, the team found that the distribution changed: caffeine monomers were much more stabilized in solution than the oligomers. Those oligomers seem to mimic the common crystal form, columnar pi-stacks of caffeine molecules, and it appears that the sugar molecules are interacting more with the two ends of these. That means that they have a much greater effect on such species as they get shorter, and on the individual caffeine molecules most of all. Interestingly, sugars like glucose, sucrose, and fructose fall along a linear relationship for this effect (sucrose, for example, acts pretty much like glucose and fructose together, as it should), while trehalose is a definite outlier. That one’s already been noted as an unusual stabilizer of macromolecules in solution (for reasons that are still being argued about), but in this case it seems that the trehalose is (compared to the others) much more excluded from the “sides” of the oligomer stacks.

This sort of “selective hydrotopy” is a new thing, so the question is how common these effects are and whether they can be anticipated. But now that we know that it’s possible, the search can commence for compounds that both associate with surfaces that are more exposed in solute monomers (such as the “tips” of the caffeine oligomers here), and are also excluded from the surfaces that are formed by the oligomers. It’ll be quite interesting to see how general this turns out to be: is it going to be mostly trehalose (which people already knew to try) or are there more things waiting out there to be found?


19 comments on “Sticking Together in Solution”

  1. Nick K says:

    I believe trehalose is found in high concentrations in tardigrades (also known as “water bears”). These organisms are astoundingly resistant to both high and low temperatures, and can survive complete dehydration. Some can even survive outer space for a few days.

    1. Teddy Z says:

      Trehalose is a common excipient in protein formulations.

    2. LdaQuirm says:

      It’s also the blood sugar for insects (instead of glucose). I haven’t specifically researched it, but I wouldn’t be surprised if it’s widespread in arthropods.

  2. Medquemist says:

    We say: insoluble “like a f***ing stone”, but also a molecule can be stable like a stone … thats is a positive adjective

  3. bioconvert says:

    why do you think small molecule research is dead these days?

    1. An Old Chemist says:

      Because in the list of the ‘Top 20 Best-Selling Drugs of the World in 2018, more than half are biologic drugs, and this is very different from what it used to be 10 plus years ago when most on this list used to be small molecules:

      1. ScientistSailor says:

        That’s by dollars, if you look at # of scripts, 49/50 of the top drugs are small-molecules, and that last one is KCl…

        1. MagickChicken says:

          And where do you think research dollars are going, to the $50/pill biologics or the $4/kg KCl?

  4. John Wayne says:

    My favorite description of the issues the formulations folks get to deal with is, “This compound is as soluble in water as a pile of rusty razor blades”

    1. Paul van den Bergen says:

      Having studied both materials and geology, statements like as soluble as a brick, as a pile of rusty razor blades, etc. make me twitch…

      Just dissolved some feldspar (for… reasons) the other day…. sure, it was in molten NaOH @ 450 oC, but still…

      (FWIW, I claim the reason I’m poor at all this messy organic stuff is that any decent heat treatment starts at 150oC and goes up from there, after which there isn’t a lot interesting left to look at… as for Paleontology…well…)

  5. cynical1 says:

    “A Spoonful of sugar helps the medicine go down
    The medicine go down
    The medicine go down
    Just a spoonful of sugar helps the medicine go down
    In a most delightful way”

    Sorry…….couldn’t resist.

  6. metaphysician says:

    “There are a range of hydrotopes known to affect caffeine’s solubility, things like urea and thiocyanate which act in many such situations. . .”

    Am I the only one whose first thought was ‘well, neither of *those* are gonna get used in a commercial product’?

    1. KazooMan says:

      Well, perhaps not for an orally administered drug, but urea is on the shelves of drug stores all over the place. It has been in a commercial health care product for decades.

  7. AM says:

    This might have changed my life. I’ll let you know tomorrow, because tomorrow I’m going to boiling some coffee grounds in sugar water to make my morning coffee…

    1. Zemyla says:

      You made a far better choice than I would have. I was thinking about coffee boiled in piss.

  8. Peter Kenny says:

    Something that does not appear to be widely known is that hydrogen bond donors are typically more easily pulled out of water than hydrogen bond acceptors. It is possible that consideration of this could help to rationalize some examples of what might appear to be weird behavior in aqueous solution. I’ve linked a recent presentation (see slides 21 through 23) and you can see that most of the polarity of the secondary amide comes from the carbonyl oxygen. This is an example of a hydrogen bond donor/acceptor asymmetry and rule of 5 (<= 5 HB donors; <=10 HB acceptors) provides a more familiar example. There are links in the slides to an article and a couple of blogs posts although you'll get the basic idea from the slides alone.

  9. Cb says:


    1. Readily soluble says:

      I guess we can always reinvent the wheel using a 3D printer and enjoy some celebrity for it.
      Oh, the things technology can do for us these days….

  10. albegadeep says:

    Did anyone else read the “sugar helps more uniformly dissolve caffeine” section and immediately think of their morning coffee?

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