Using NMR for ligand discovery and optimization Hugo O Villar  , Jiangli Yan and Mark R Hansen Several recent technology-driven advances in the area of NMR have rekindled an interest in the application of the technology to problems in drug discovery and development. A unique aspect of NMR is that it has applicability in broadly different areas of the drug discovery and optimization processes. NMR techniques for screening aimed at the discovery of novel ligands or low molecular weight structures for fragment- based build up procedures are being applied commonly in the industry. Application of NMR in structure-guided drug design and metabonomics are also becoming routine. We present an overview of some of the most recent NMR developments in these areas. Addresses Triad Therapeutics, 9381 Judicial Dr., San Diego, California 92121, USA  Current address: Altoris, Inc., 5820 Miramar Rd- Suite 207, San Diego, CA 92121, USA e-mail: hugo@altoris.com Current Opinion in Chemical Biology 2004, 8:387–391 This review comes from a themed issue on Next-generation therapeutics Edited by Tudor Oprea and John Tallarico Available online 5th June 2004 1367-5931/$ – see front matter ß 2004 Elsevier Ltd. All rights reserved. DOI 10.1016/j.cbpa.2004.05.002 Abbreviations ADME availability, distribution, metabolism and excretion SAR structure–activity relationship STD saturation transfer difference WaterLOGSY water–ligand observed via gradient spectroscopy Introduction The momentum gathered by NMR as an essential tool in drug discovery is witnessed by the ever increasing num- ber of articles reviewing its application [1  ,2–4]. Its newest evolution reflects a shift from the use of NMR as a tool for structure determination and more into a tool for screening with structural information embedded in it. Methods such as structure–activity relationship (SAR)- by-NMR [5,6] and the SHAPES [7] procedure led the way for several developments in the field largely with respect to the strategies for application of NMR. NMR has several features that make it particularly effec- tive in drug discovery. It provides structural information about the binding mode of a ligand in solution, the possibility of carrying out screening in the presence or absence of a cofactor, different protein activation states or environmental conditions. Compared with high-through- put screening techniques, it has little tendency to give false positives. NMR can be used to quickly identify ligands of low affinity, which has provided a new avenue for the identification of novel ligands for a target of interest. Those weak ligands can be used to bias virtual screening, as scaffolds in combinatorial approaches, or in ligand build-up, or fragment-based procedures. Moreover, its applicability to problems in metabonomics and toxicology makes it a very powerful ally in the process of drug development. NMR is one of the few techniques with such broad applicability throughout the drug dis- covery and optimization process and even in clinical studies. Its use in lead discovery via fragment assembly methods, in structure- guided ligand optimization and the developments in availability, distribution, metabolism and excretion (ADME) and toxicological studies are positioning it as an indispensable tool. This broad applic- ability arises because NMR is a modular technology that can be customized for diverse purposes. Within the umbrella of NMR, many different processes that involve the interaction between a small organic molecule and a protein can be monitored. In the following sections we attempt to summarize some of the most recent developments in the field, without covering the on-going research in structural determina- tion or proteomics using NMR [8], which have some significant bearing for lead discovery and optimization as well. NMR and screening Figure 1 is an attempt to condense the processes currently favored in lead discovery by NMR. Typically, the initial step is the screening of a small collection of low molecular weight molecules that can be used as either scaffolds or prosthetic groups in the design of a novel ligand, similar to the initial steps in SAR-by-NMR or the SHAPES procedure. An interesting example uses focused libraries that com- bine small molecules containing structural elements found in known drugs, protease inhibitors and substruc- tures present in factor Xa inhibitors. These were used to uncover new leads for factor Xa, using saturation transfer difference (STD) experiments [9]. Beyond the already established procedures, significant advances continue to be made in the use of NMR for lead discovery purposes. A very attractive approach has been www.sciencedirect.com Current Opinion in Chemical Biology 2004, 8:387–391