1. Introduction 211
2. Screening methods 213
2.1 Chemical shifts 213
2.2 Diffusion 214
2.3 Transverse relaxation 218
2.4 Nuclear Overhauser effects 218
3. Strategies for drug discovery and design 221
3.1 Fragment-based methods 221
3.1.1 Linked-fragment approach 221
3.1.2 Directed combinatorial libraries 222
3.1.3 Modification of high-affinity ligands 223
3.1.4 Solvent mapping techniques 223
3.2 High-throughput NMR-based screening 224
3.3 Enzymatic assays 226
4. Discovery of novel ligands 227
4.1 High-affinity ligands for FKBP 227
4.2 Potent inhibitors of stromelysin 229
4.3 Ligands for the DNA-binding domain of the E2 protein 233
4.4 Discovery of Erm methyltransferase inhibitors 233
4.5 Phosphotyrosine mimetics for SH2 domains 236
5. Conclusions 237
6. References 237
A critical step in the drug discovery process is the identification of high-affinity ligands for
macromolecular targets. Traditionally, the identification of such lead compounds has been
accomplished through the high-throughout screening (HTS) of corporate compound
repositories. Conventional HTS methodology has enjoyed widespread application and
success in the pharmaceutical industry and, through recent technological advances in
screening (Fernandes, 1998; Oldenburg et al. 1998; Silverman et al. 1998) and combinatorial
chemistry (Fauchere et al. 1998; Fecik et al. 1998), these programs will continue to have a
prominent role in drug discovery. However, suitable leads cannot always be found using
conventional methods. This is not surprising since typical corporate libraries contain fewer
than 106 compounds compared with the estimated 1050–1080 universe of compounds (Martin,
1997). In addition, most conventional assays are limited to screening libraries of compounds
against proteins with known function, excluding the large number of targets becoming
available from genomics research.
Recently, a number of NMR-based screening methods have been employed to identify
and design lead ligands for protein targets (see Table 1). These NMR-based strategies can
augment ongoing conventional HTS for identifying leads and can be used to aid in lead
optimization. All of these techniques take advantage of the fact that upon complex formation
between a target molecule and a ligand, significant perturbations can be observed in NMR-sensitive parameters of either the target or the ligand. These perturbations can be used
qualitatively to detect ligand binding or quantitatively to assess the strength of the binding
interaction. In addition, some of the techniques allow the identification of the ligand binding
site or which part of the ligand is responsible for interacting with the target. In this article,
the current state of NMR-based screening is reviewed.