Designing fragment libraries

The topic of fragment library design is similar to foundation construction: most people don’t give it much thought, but any organization that doesn’t take it seriously could quickly find itself on shaky ground. Three recent papers cover different aspects of this topic.

The first paper, published in J. Comput. Aided Mol. Des. by researchers at Pfizer, describes the design and construction of their Global Fragment Initiative (GFI), a 2,885 fragment library meant to be broadly applicable to any target using any screening method (NMR, X-ray, SPR, MS, and biochemical assays). Most of these fragments came from commercial or in-house collections, but 293 were synthesized specifically for the library. All compounds were filtered to remove reactive or otherwise undesirable moieties. Interestingly, a large number of cationic and anionic molecules were included, based on the observation that many approved drugs are charged. Also, roughly a quarter of the compounds contained at least one chiral center.

Potential library members were put through a rather more rigorous selection than the standard Rule of 3 (for example, cLogP < 2.0). Molecular complexity was explicitly considered, and overly complex fragments were excluded. Fragments were also analyzed by 2D and 3D similarity and chosen to maximize diversity, though with the criterion that close analogs were available either in-house or commercially. Compounds were also chosen to allow rapid chemical elaboration. Finally, compounds were evaluated by NMR for purity and solubility at 1 mM in aqueous buffer and 50-100 mM in DMSO.

The bulk of the library (excluding custom-synthesized fragments) has been screened against at least 13 targets in 8 different protein families, mostly by NMR and biochemical assays, resulting in hit rates between 2.8 – 13%. Only one fragment hit all 13 targets, while 766 hit only one; in total 33% of the fragments hit one or more of the targets, a fraction eerily similar to that seen at Genentech and Vernalis. Overall this is a thorough, information-dense paper, and well worth reading if you are considering building or expanding a fragment library.

One of the most productive first steps you can take after identifying a fragment hit is to test close analogs or larger molecules that contain the fragment. Of course, it is easier to buy compounds than to make them, so a fragment library that effectively samples commercial compounds is likely to be useful. This “SAR by catalog” approach is the topic of the second paper, also in J. Comput. Aided Mol. Des., from Rod Hubbard and colleagues at Vernalis and the University of York.

The researchers analyzed catalogs of available compounds from each of three vendors (Asinex, Maybridge, and Specs). Filtering out undesirable functionalities and binning the molecules by size left 5600-7700 fragment-sized molecules and 28,600-252,000 larger molecules per vendor. Compound properties of the fragment sets (MW, polar surface area, number of hydrogen bond donors and acceptors, etc.) are summarized for each of the vendors, similarly to Chris Swain’s analysis. Six different algorithms were then tested to find sets of 200 fragments that would best represent the entire collection. In accordance with Murphy’s Law, the most complicated algorithm proved to be the most effective; it involves an iterative selection procedure with precisely defined similarity criteria. Still, this algorithm is not too difficult to implement, and it should prove a useful tool for selecting fragments from larger sets of commercial or in-house compounds.

Finally, a chapter by James Na and Qiyue Hu at Pfizer in a recent volume of Methods in Molecular Biology gives a broad overview of fragment library design. In addition to general considerations, the paper succinctly summarizes the design of the Pfizer Global Fragment Initiative as well as an earlier fragment library designed specifically for NMR screening. A more lengthy but instructive description of several Vernalis fragment libraries is also provided, as are some of the screening results. Finally, a nice table summarizes fragment libraries from more than a dozen companies.