Recent Developments in Fragment-Based Drug Discovery

Abstract

The field of fragment-based drug discovery (FBDD) has developed significantly over the past 10 years and is now recognized as a tangible alternative to more traditional methods of hit identification, such as high throughput screening (HTS). The number of commercial and academic groups actively engaged in fragment-based research has increased, and as a consequence, there has been continued development and refinement of techniques and methods. From its inception, the fragment-based approach had two central tenets that were critical to its success and that have set it apart from HTS and other hit identification techniques. The first is the concept that chemical space can be more efficiently probed by screening collections of small fragments rather than libraries of larger molecules. The number of potential fragments with up to 12 heavy atoms (not including threeand four-membered ring structures) has been estimated at 10, whereas the number of potential druglike molecules with up to 30 heavy atoms is estimated at more than 10. Therefore, a much greater proportion of “fragment-like” chemical space can feasibly be screened in FBDD compared to “druglike” chemical space covered in a HTS where molecular size is much larger. The second idea is that, because by definition fragment molecules are small in size (typically less than 250 Da), they should typically bind with lower affinity to their target protein (micromolar to millimolar range) compared with druglike molecules that can form many more interactions (nanomolar to micromolar range) but that the binding efficiency per atom is at least as high as for larger hit molecules. Implicitly, the screening techniques employed in FBDD must be correspondingly much more sensitive than a HTS bioassay. Generally, sensitive biophysical techniques are employed to detect these weak binding events and to characterize the fragment interactions with the target active site. Nuclear magnetic resonance (NMR) and protein X-ray crystallography have been used extensively in fragment-based research because these techniques are highly sensitive in detecting low affinity fragment binding and also give information about the fragmentprotein interactions being formed. There have been a number of recently published general review articles that have discussed the various aspects of the FBDD field. In addition, there are now two books on the subject. In this journal in 2004, Erlanson et al. summarized the major developments in FBDD since the original publication by Fesik and co-workers of the “SAR by NMR” approach in the late 1990s. Particular note was given to the biophysical methods employed to screen for fragment binding and the merits and drawbacks of each of these techniques, along with the approaches that can be used to optimize fragments into lead molecules. Herein, the trends and developments over the past 4 years will be outlined and some selected examples that are illustrative of the approaches being utilized by those active in the field examined. Additionally, this review will look in some detail at representative protein-ligand complexes observed between fragment-sized molecules and their protein targets from the Protein Data Bank (PDB). Finally, some conclusions will be drawn from these data and the future of FBDD discussed.