Protein X-ray Crystallography and Drug Discovery

Abstract

With the advent of structural biology in the drug discovery process, medicinal chemists gained the opportunity to use detailed structural information in order to progress screening hits into leads or drug candidates. X-ray crystallography has proven to be an invaluable tool in this respect, as it is able to provide exquisitely comprehensive structural information about the interaction of a ligand with a pharmacological target. As fragment-based drug discovery emerged in the recent years, X-ray crystallography has also become a powerful screening technology, able to provide structural information on complexes involving low-molecular weight compounds, despite weak binding affinities. Given the low numbers of compounds needed in a fragment library, compared to the hundreds of thousand usually present in drug-like compound libraries, it now becomes feasible to screen a whole fragment library using X-ray crystallography, providing a wealth of structural details that will fuel the fragment to drug process. Here, we review theoretical and practical aspects as well as the pros and cons of using X-ray crystallography in the drug discovery process.

Keywords: X-ray crystallography; drug discovery; high resolution; ligand screening; protein-ligand complexes; structure-based drug design; therapeutic targets; three-dimensional structures.

Figure 1

The drug design cycle. Steps in dashed boxes are not mandatory in the early stage of drug development. Contributions of X-ray crystallography are indicated with schematic crystals. Abbreviations: FBLD, fragment-based ligand/lead discovery; FBDD, fragment-based drug discovery.

Figure 2

Weakly bound fragments can easily be overlooked. Comparison of maps obtained using the PanDDA procedure (a, c) or after standard refinement (b, d). Diffraction data were collected from 839 crystals of an in-house target, each obtained in the presence of a distinct fragment (unpublished results). One specific dataset from this ensemble is shown (resolution of 1.3 Å). Although the water molecules displayed in (b) and (d) were also included in the model fed to the PanDDA procedure, they were not included in (a) and (c) to improve clarity. The PanDDA event map (a, contoured at 1 σ, BDC = 0.88) and the Z-map (c, green/red ±3 contour level) clearly show the presence of the fragment. Standard 2mF_o-DF_c (b, 1 σ contour level) and mF_o-DF_c (d, green/red ±3 σ) electron density maps, obtained after preliminary refinement (R/R_free 0.172/0.193), fail to indicate fragment binding. All maps were carved 5 Å around the position of the bound fragment. For a definition of BDC and Z-map, please refer to [62].