FBLD started early at AstraZeneca (AZ). The first conference Practical Fragments covered was held at their erstwhile Alderley Park site; Pete Kenny is an AZ alum, and the company has put at least four fragment-derived drugs into the clinic. Clearly their scientists have learned plenty about what works and what doesn’t, and much of this wisdom is distilled into an excellent recent review in Drug Discovery Today. The authors include Nathan Fuller, Joe Patel, and Lorena Spadola, the first two of whom are organizers for the upcoming FBLD 2016 – for which there is still just barely time to register.
Things weren’t easy in the beginning: of the 63 FBLD targets screened between 2002 and 2008, a mere 10% led to tractable lead series with interpretable SAR. This improved to 37% of the 19 campaigns conducted between 2009 and 2011, and to 64% of the 11 projects between 2012 and 2014.
What accounts for these improvements? Target selection certainly played a role. In earlier years many targets were dropped due to portfolio reasons or lack of validation – nearly half for the period 2009-2011. Often FBLD was tried in desperation when all else failed, and chemists were not always available for fragment-to-lead efforts. Today, fragment screening is considered for all water-soluble targets at AZ, and fully integrated teams are brought into the process earlier. In 2012 the company established a team of medicinal chemists dedicated to FBLD – a strategy that has also been used at other companies.
But many of the improvements are technological rather than organizational. Biophysical screens are displacing high-concentration biochemical screens, which are particularly prone to false positives and false negatives. 1D and 2D NMR remain mainstays, but SPR and X-ray crystallography are increasingly being used in primary screens.
Another major effort was revamping the fragment library, which currently stands at 15,000 members. Each fragment was experimentally confirmed to be soluble to at least 0.5 mM in water and 100 mM in DMSO, and the rule of three was used more as a guideline than a rule. The collection was designed to include a good proportion of “three-dimensional” fragments, as assessed by plane of best fit (PBF) and principal moment of inertia (PMI). About a quarter of the fragments are proprietary, and the company also has another 750,000 molecules within their corporate collection that could be classified as fragments, greatly facilitating follow-up studies.
A 15,000 member library is atypically large, but in practice smaller subsets of the library are deployed: 384 for crystallographic screening, 1152 for NMR screening, and 3072 for SPR screening. Each subset is optimized for the technique. For example, because the crystallographic subset is so small, it is designed to sample chemical space as efficiently as possible. This is done by maximizing the diversity of the fragments and choosing the smallest fragments possible – less than 17 non-hydrogen atoms, as at Astex. In contrast, the NMR and SPR subsets contain fragments having up to 21 non-hydrogen atoms, and the SPR set also contains close analogs of some fragments to improve confidence and provide preliminary SAR. There is some overlap between the sets to facilitate confirmation; for example, a 768-member “ligandability set” is shared between the NMR and SPR screening libraries. Finally, AZ has built a customized set of 800 covalent fragments.
For the most part, fragment hits from each subset tend to have similar properties as the subset in general, suggesting that each sub-library is well-suited for its technique. Importantly, this is true even for three-dimensional fragments, which comprise nearly half of the hits across 19 targets. The researchers also examined how effectively fragments were able to fill the volume of a given binding pocket for five targets with multiple crystal structures. They found that shapely fragments were at least as good as – and sometimes better – at filling the pockets, even with fewer three-dimensional fragments.
Finally, the article summarizes eight projects in which fragment hits were progressed. Dissociation constants for the hits ranged from 50 to 3230 µM; these were advanced to leads with affinities ranging from 1.5 to 180 nM. In half these cases the ligand efficiency improved, and in all cases the three dimensionality increased as defined by PBF. Two of the targets, phosphoglycerate dehydrogenase and mInhA, are discussed in some detail, complete with chemical and crystal structures. Hopefully all will be covered more fully in upcoming publications.
There’s lots more in this paper than I can summarize in a blog post, including multiple figures and tables, so definitely check it out.