29 April 2011

Not fragments versus DOS, fragments from DOS

A few months ago we highlighted a forum in Nature comparing fragment-based lead discovery with diversity-oriented synthesis, or DOS. This was quite a vigorous debate and was covered on our sister blog as well as In the Pipeline and second messenger. Personally I’ve never been a this or that kind of guy – more of a this and that – so it is refreshing to see a paper in this week’s issue of PNAS describing a DOS approach to building fragments.

Damian Young and colleagues at Harvard and the Broad Institute, ground zero for DOS, noted that many commercial fragments contain a sizable percentage of sp2 carbons: aromatic rings, for example. Because a larger number of aromatic rings correlates with lower solubility and higher attrition in lead development, the researchers focused on using DOS to generate fragments that would have a higher fraction of sp3 carbons at the expense of sp2 carbons. They used a “build/couple/pair” approach, in which chiral “building blocks” (in this case proline derivatives) were “coupled” to another building block and then functional groups were “paired” to generate bicyclic molecules. The result was about three dozen fragments.

So how do they look? Actually, not so bad. Superficially they all resemble one another, but because they contain up to three stereocenters they cover quite a bit of chemical space while still conforming to the rule of 3. Significantly, they are in fact more three-dimensional than commercially available fragments (from ZINC) having the same molecular formula or the same set of calculated physical properties (molecular weight, cLogP, number of hydrogen-bond donors and acceptors, etc.). The DOS fragments contain a larger fraction of methyl esters and carboxylic acids than I would want to see in a library overall, but this was intentional, and none of them are downright ugly.

Unfortunately the paper provides no screening data, so it is anyone’s guess whether any of the fragments will turn out to be active. Still, the approach is likely to probe new areas of chemical space. Hopefully some of the commercial purveyors of fragments will start making and selling these types of molecules.

23 April 2011


The sequencing of the human genome has thrown up lots of potential targets, but choosing which ones to pursue is difficult: many are not biologically relevant and many are shaped such that small molecules are unable to affect their activity. “Druggability” is a popular neologism that captures both of these ideas; it refers to whether a protein can be targeted by a small molecule – preferably an orally bioavailable one – to treat a disease. However, the two components of druggability are really separate concepts, and in this month’s issue of Drug Discovery Today Fredrik Edfeldt, Rutger Folmer, and Alex Breeze coin a new term – “ligandability”. A protein is ligandable if potent small-molecule ligands can be found for it. Obviously for a protein to be druggable it needs to be ligandable, and thus it would be nice to assess this characteristic as quickly as possible. How can this be done?

Enter fragments. Because fragments have lower complexity than lead-sized (let alone drug-sized) molecules, hit rates from fragment screens tend to be higher. If a binding pocket exists in a protein, a small library of just 1000 fragments or so should produce a good range of hits. In fact, Phil Hajduk and colleagues at Abbott found several years ago that fragment screens predict the success of lead discovery campaigns. In the new paper, Edfeldt and colleagues, all at AstraZeneca, analyzed 36 internal discovery projects where both fragment screens and HTS had been conducted. They used data from the fragment screens to categorize targets into three ligandability bins:
  • Low: low hit rate, best affinities > 1 mM, low diversity of hits
  • Medium: intermediate hit rate, best affinities 0.1 – 1 mM, some diversity of hits
  • High: high hit rate, best affinities < 0.1 mM, high diversity of hits
Remarkably, all 12 targets with a low ligandability score failed HTS. Of targets that scored medium or high ligandability, 17/24 were successful in HTS screens, and 20/24 were advanced into hit-to-lead studies. These successes include targets such as BACE1 (medium ligandability), which failed HTS but which led to potent leads using fragment-based approaches. Of course, a ligandable protein may still not be druggable if it is ultimately not essential for a disease, but you often don’t discover this until after years of clinical trials.

AstraZeneca is now using fragment-based ligandability screening to help assess which targets to pursue: those with low ligandability are only pursued when the biology is truly compelling. On the flip side, targets that have failed conventional HTS but have high ligandability are reexamined using alternative hit discovery techniques, such as fragment-based methods. This seems like an appealing approach: fragments not only help drug hunters avoid throwing out the baby with the bathwater, but also to avoid drowning in dirty bathwater. I wonder how many other companies are using similar strategies.

15 April 2011

Sixth Annual Fragment-Based Drug Discovery

The only US-based conference completely devoted to fragment-based drug discovery ended in San Diego this week. As with last year, I won’t attempt to summarize all of the talks – there was far more information presented than I have time to write (or that you probably have patience to read!) For those of you who were there, please feel free to mention some of the things I missed.

One of the points that Don Huddler (GlaxoSmithKline) and I (Carmot) made in the pre-conference short-course is that finding fragments is a solved problem. As Rod Hubbard (Vernalis, University of York) noted in his opening presentation, “it’s pretty simple to find fragments that bind; a graduate student can do it in a couple months.” Even membrane proteins are starting to yield to fragment-based screening, as Gregg Siegal (ZoBio, Leiden University) discussed in his closing session (see also here).

That’s not to say that new methods for finding fragments aren’t useful, particularly if they open new target space, are faster or more reliable, or provide new information. An example of the latter was the presentation by Denis Zeyer (NovAliX) on native mass-spectrometry (see also here). Because hydrophobic interactions are weaker in the gas phase than in water, it should be possible to select for molecules that bind predominantly through polar interactions. In fact, by gradually increasing the voltage in their MS instrument, Zeyer and colleagues generated “VC50” curves, the voltage at which half the compound dissociates from the protein. At least in one case, a higher VC50 correlated with the presence of an additional hydrogen bond to the protein compared with related molecules.

Polar contacts are generally associated with enthalpic rather than entropic interactions, and whether such fragments are preferable was the subject of some discussion, particularly at a breakfast round-table discussion. In contrast to a meeting just last year, several participants were actively collecting thermodynamic data, though there was some uncertainty as to what to do with it. This is a controversial subject; one person suggested that enthalpic binders are likely to be more hydrophilic than entropic binders, so just keeping an eye on lipophilicity is likely to be just as useful and far easier than actually measuring thermodynamic parameters. Charles Reynolds (Ansaris) provided an analysis that illustrates some of the difficulties in using thermodynamic data – I’ll follow up on this in a later post.

The shape of fragments has been previously discussed, and Ivan Efremov (Pfizer) gave a nice case study of a strikingly three-dimensional fragment: an X-ray screen of 340 molecules against BACE resulted in a single hit, a spirocyclic pyrrolidine. The electron density of this was so clear that it didn’t even need to be deconvoluted from the other three compounds in the pool, and medicinal chemistry ultimately led to low micromolar inhibitors.

There was general consensus that ligand efficiency (and various lipophilicity adjusted versions) is a helpful metric. One practitioner said that his company had sometimes pursued more chemically tractable but less ligand efficient fragments and generally came to regret those decisions. But a fragment with lower ligand efficiency could still be interesting: with fragments, even small changes could have huge effects on binding (see for example AT13387, which was discussed by Chris Murray of Astex). Thus, a bit of initial fragment optimization could be a good investment before pursuing more intensive chemistry, particularly if commercial or in-house analogs are available. Interestingly, I couldn’t find anyone who uses either fit quality or %LE.

In the early days of fragment-based lead discovery a common selling point was that it sped up drug discovery, but a theme in this meeting was that it is not necessarily faster but can provide leads against more difficult targets or better leads against “normal” targets. Of course, one has to be wary of taking a good fragment, slapping a bunch of grease on it, and turning it into a lipophilic monster.

Indeed, an analysis of fragment-derived leads published a couple years ago was not flattering. Taking up the thrown gauntlet on behalf of fragments, Chris Murray presented a retrospective analysis of all 42 fragment to lead programs at Astex (including 21 kinases and 9 proteases). The average parameters of these leads were considerably more attractive in terms of both molecular weight and ClogP that the published values of the HTS hits. At least according to this analysis, fragment approaches have the potential to deliver superior molecules, as long as one is disciplined and creative in how these approaches are applied.

07 April 2011

Wedding announcement: SuperGen and Astex

It’s wedding season in the world of fragments – last month we noted the merger of Daiichi Sankyo and Plexxikon, and today SuperGen and Astex Therapeutics announced that they are tying the knot. Unfortunately the “dowry” in this case is considerably smaller: SuperGen will pay Astex shareholders $25 million cash upfront, with an additional $30 million in deferred payments. Astex shareholders will, however, still retain 35% equity in the combined company.

Astex has long been a leader in fragment-based drug discovery, having taken at least three programs from fragments to clinical compounds (see blog entries on AT13387, AT9283, and AT7519). Perhaps it is in recognition of this that the combined entity will be called Astex Pharmaceuticals. Practical Fragments wishes everyone involved the best of luck.

01 April 2011

Fragments in vivo

The number of ways to find fragments just keeps growing. A few weeks ago we discussed WAC, which takes its place alongside ITC, SPR, MS, TINS, and more traditional methods such as NMR, X-ray and biochemical screening. However, all of these approaches are somewhat reductionist, relying on isolated target proteins. In an effort to bring the whole organism into the picture, our friends at the University of Shutka, Russia, have come up with an approach they call “Fragments in Bodies,” or FIB.

The researchers have assembled a collection of very small fragments, purchased for the most part from Lilliput Pharmaceuticals. These are then screened in mouse models to look for positive phenotypic effects.

The researchers face some unique challenges. For example, it is difficult to measure changes in body mass as the animals need to consume such large amounts of fragments that they can become somewhat bloated. Still, if the animals can be safely dosed with massive amounts of micro-molecules, "FIB"ing could provide very good starting points for further work!