FBDD Down Under

Fragment-Based Drug Design Down Under was held at Monash University in Melbourne, Australia earlier this month. The first dedicated FBDD conference in this country was full of enthusiasm: I had the impression many of the 100 or so participants, most of them Australian, were happily surprised to meet so many other fragment aficionados. With 18 oral presentations, nearly as many posters, and a lively panel discussion I can only touch on some of the broader themes here, so please weigh in with your own observations.

Fragment library design received considerable attention, which was nice as this is an area that is all too often ignored in conferences. Pete Kenny's name came up a couple times in helping to put together the CSIRO fragment library. Craig Morton gave an excellent overview of the SVIMR fragment library and some of the challenges constructing it: of roughly 1600 fragments purchased, 450 were either not sufficiently soluble in water or DMSO or not sufficiently pure to be included. David Chalmers of MIPS presented an analysis of the physicochemical properties of approved drugs, noting that roughly three quarters are ionizable, with potential implications for library design.

Three dimensional fragments have been much discussed lately, and Martin Drysdale of the Beatson Institute described a UK consortium, 3Dfrag.org, to put together a library of 3-dimensional fragments, as defined by having a principal moment of inertia closer to a sphere (think adamantane) as opposed to a plane (benzene) or a rod (2-butyne). The project is still in its early stages, with about 200 fragments acquired thus far. Martin also described an interesting collaboration with the Broad Institute to use existing DOS-derived fragment-sized molecules for screening.

There were several talks on fragment screening methods, especially NMR and SPR. In an intriguing comparison, Jerome Wielens of SVIMR described parallel efforts on HIV integrase, both using essentially the same (Maybridge) library. STD NMR screening produced more than 50 hits, ultimately yielding 15 co-crystal structures, while SPR screening (also discussed later by Tom Peat of CSIRO) produced 16 hits and ultimately 6 crystal structures, yet few of the hits were in common. There were differences in the protein constructs and pH, and some of the NMR hits may have been artifactual, while the use of a reference protein in SPR may have weeded out some true positives. All of which underlines the fact that using multiple biophysical methods is ideal.

STD NMR came under scrutiny from others as well: San Lim of MIPS described compounds that showed a signal when screened in mixtures but not when tested individually, and Martin Drysdale discussed one target that gave a 36% hit rate using the technique, leading him to pick SPR as a primary screening method. Still, there are some interesting possibilities: Thomas Haselhorst of Griffith University discussed using STD NMR not just for screening membrane proteins but for screening viruses, cells, and even fungal spores!

Markku Hämäläinen of GE Healthcare discussed the use of both SPR (specifically Biacore) and ITC. In the case of SPR, he termed one class of problematic compounds “selective promiscuous binders”: for example, a positively charged protein may cause negatively charged fragments to aggregate around it, giving anomalously high signals. Using a positive control and setting a maximum Rmax in fitting the data can help weed these out and provide more accurate dissociation constants. In a collaboration with Merck Serono on a kinase target, 105 hits from a 1920-fragment library gave an 80% confirmation rate when tested in ITC, and 41 of 48 produced co-crystal structures.

But as we are increasingly seeing, Biacore is no longer the only name in the SPR game: Olan Dolezal of CSIRO described Bio-Rad’s ProteOn instrument and found that, while it was less sensitive than Biacore, its higher throughput made it an attractive primary screening instrument.

There were also a couple interesting talks on in-situ methods for fragment assembly, including MS-based methods described by Sally-Ann Poulsen of Griffith and click-based methods discussed by William Tieu at the University of Adelaide. One of the problems with assembling a high-affinity molecule in situ is product release: a molecule made in situ might bind so tightly it never leaves the protein, which essentially stops production once a stoichiometric amount of the inhibitor is made. In Tieu’s case, the problem was cleverly overcome by introducing a mutation to lower the affinity.

Finally, Jonathan Baell of MIPS gave an excellent (though disturbing) talk on PAINS – a topic which is still unfortunately not sufficiently appreciated. In one illuminating example, he found that an in-house screen of a histone acetyltransferase produced only a single legitimate hit, along with a plethora of PAINS.

One common theme both in the presentations and offline discussions was the relative lack of chemistry support; definitely a pity, since there are certainly plenty of chemists looking for new opportunities. Of course, funding chemistry is a problem not unique to the Southern Hemisphere.

Australia is clearly a new world for fragments, and it will be fun to see how the field develops there. And on a personal note, I found Aussies to be some of the warmest, most genuine people I have met in any country. I definitely look forward to finding an excuse to return.