Skip to Content

These Fragments I Have Shored Against My Ruins

There’s been a big trend the last few years in the industry to try to build our molecules up from much smaller pieces than usual. “Fragment-based” drug discovery is the subject of many conferences and review articles these days, and I’d guess that most decent-sized companies have some sort of fragment effort going on. (Recent reviews on the topic, for those who want them).
Many different approaches come under that heading, though. Generally, the theme is to screen a collection of small molecules, half the size or less of what you’d consider a reasonable molecular weight for a final compound, and look for something that binds. At those sizes, you’re not going to find the high affinities that you usually look for, though. We usually want our clinical candidates to be down in the single-digit nanomolar range for binding constants, and our screening hits to be as far under one micromolar as we can get. In the fragment world, though, from what I can see, people regard micromolar compounds as pretty hot stuff, and are just glad not to be up in the millimolar range. (For people outside the field, it’s worth noting that a nanomolar compound binds about a million times better than a millimolar one).
Not all the traditional methods of screening molecules will pick up weak binders like that. (Some assays are actually designed not to read out at those levels, but to only tell you about the really hot compounds). For the others, you’d think you could just run things like you usually do, just by loading up on the test compounds, but that’s problematic. For one thing, you’ll start to chew up a lot of compound supplies at that rate. Another problem is that not everything stays in solution for the assay when you try to run things at that concentration. And if you try to compensate by using more DMSO or whatever to dissolve your compounds, you can kill your protein targets with the stuff when it goes in. Proteins are happy in water (well, not pure distilled water, but water with lots of buffer and salts and junk like the inside of a cell has). They can take some DMSO, but it’ll eventually make even the sturdiest of them unhappy at some point. (More literature on fragment screening).
And once you’ve got your weak-binding low-molecular weight stuff, what then? First, you have to overcome the feeling, natural among experienced chemists, that you’re working on stuff you should be throwing away. Traditional medicinal chemistry – analog this part, add to that part, keep plugging away – may not be the appropriate thing to do for these leads. There are just too many possibilities – you could easily spend years wandering around. So many companies depend on structural information about the protein target and the fragments themselves to tell them where these little guys are binding and where the best places to build from might be. That can come from NMR studies or X-ray crystal determinations, most commonly.
Another hope, for some time now, has been that if you could discover two fragments that bound to different sites, but not that far from each other, that you could then stitch them together to make a far better compound. (See here for more on this idea). That’s been very hard to realize in practice, though. Finding suitable pairs of compounds is not easy, for starters. And getting them linked, as far as I can see, can be a real nightmare. A lot of the linking groups you can try will alter the binding of the fragments themselves – so instead of going from two weak compounds to one strong one, you go from two weak ones to something that’s worse than ever. Rather than linking two things up, a lot of fragment work seems to involve building out from a single piece.
But that brings up another problem, exemplified by this paper. These folks took a known beta-lactamase inhibitor, a fine nanomolar compound, and broke it up into plausible-looking fragments, to see if it could have been discovered that way. But what they found, each time they checked the individual pieces, was that each of them bound in a completely different way than it did when it was part of the finished molecule. The binding mode was emergent, not additive, and it seems clear that most (all?) of the current fragment approaches would have been unable to arrive at the final structure. The authors admit that this may be a special case, but there’s no reason to assume that it’s all that special.
So fragment approaches, although they seem to be working out in some cases, are probably always going to miss things. But hey, we miss plenty of things with the traditional methods, too. Overall, I’m for trying out all kinds of odd things, because we need all the help we can get. Good luck to the fragment folks.

7 comments on “These Fragments I Have Shored Against My Ruins”

  1. Jose says:

    I am not all that surprised about fragments binding in odd ways- on an old kinase project, we had compounds in the same series flip 180 degrees in the X-ray structures.
    By the by, Eliot had a whole theory about the “catalysis of poetics,” so it comes full circle.

  2. Derek Lowe says:

    Jose, I’m glad that someone picked up on the quote. I’ve got a picture of me from my senior year in college, sitting next to a gravity silica gel column and reading Eliot. I should scan it and post the darn thing.

  3. milkshake says:

    This reminds me when I was working at a combichem company they found a short peptide hit that turned into useful lead. Later when they have made some similar new libraries for the same target and they on purpose included the building blocks so that they have that hit in the present in the library, as a control. They didn’t find it the second time.

  4. A Nonie Mouse says:

    My question regarding the beta-lactamase inhibitor is if joining the fragments in this new way would lead to an active compound? I don’t think the test should be a for particular compound to be re-findable by a fragment method – does it really surprise people that some compounds bind in an emergent manner?

  5. Bacon says:

    What is your opinion of Ellman’s method for screening fragment substrates that are converted to inhibitors? I’m in his department (might therefore be biased), but it seems that it is quite efficient for relevant enzymes (proteases and phosphatases). Thoughts?

  6. Sili says:

    For a moment there I got my hopes up.
    Too bad chemical crystallographers who actually finished their Ph.D. are thirteen to the dozen.
    And I don’t know the first thing about protein work either …

  7. Its fantastic as your other articles : D, thanks for putting up. “Even Albert Einstein reportedly needed help on his 1040 form.” by Ronald Reagan.

Comments are closed.