Leveraging structural approaches: applications of NMR-based screening and X-ray crystallography for inhibitor design

Abstract

In the last several years, NMR strategies in drug discovery have evolved from a primarily structural focus to a set of technologies that are non‐structural in nature but that have a much greater impact on the identification and optimization of real drug leads. NMR‐based screening methods, such as the SHAPES strategy, help rapidly identify good starting points for drug design in a relatively high throughput implementation. The SHAPES method uses simple NMR techniques to detect binding of a limited, but diverse library of low molecular weight, soluble compounds to a potential drug target. SHAPES library compounds are derived largely from molecular frameworks most commonly found in known therapeutic agents. The NMR experiments used in these protocols are based on the well‐known NMR techniques, and may be applied to targets with no limitation on molecular weight and no requirement for isotope labeling. Following screening, SHAPES hits may be used to guide virtual screening, synthesis of combinatorial libraries, and bias the first compounds that undergo high throughput screening. Integration of the SHAPES strategy with iterative X‐ray crystallographic structure determination can be very useful in deriving an initial structural pharmacophore model and achieving significant in vitro potency in a short time frame. Here, examples are provided of how the combination of NMR SHAPES screening, virtual screening, molecular modeling and X‐ray crystallography has led to novel drug scaffolds in several drug discovery programs: JNK3 MAP kinase and the fatty acid binding protein, aP2.

Design of Inhibitors for S100B

“…Often, such techniques depend on detailed structural knowledge of the target and are the most robust, but require more protein than fluorescence studies. NMR strategies are also used in conjunction with crystallography and virtual screening methods to obtain and optimize lead compounds [130,131]. One popular NMR method is coined the name SAR (structure activity relationship) by NMR [132].…”

Functional Genomics and NMR Spectroscopy

“…The design and composition of the chemical library is a major component of the SHAPES approach to screening by NMR [205][206][207]. The SHAPES library is a small, structurally diverse library composed of water soluble compounds that correspond to fragments or molecular frameworks of known drugs.…”

Determining the optimal size of small molecule mixtures for high throughput NMR screening

“…Conversely, chemical libraries screened by NMR have a high likelihood of having hit rates > 5%. First, NMR is increasingly using small directed libraries with increased drug-like characteristics and a higher propensity to bind a protein because of the limited throughput of NMR screens compared to traditional HTS (Fejzo et al, 1999;Johnson et al, 2003;Lepre et al, 2002;Moore et al, 2004). Second, NMR screens tend to be more sensitive than traditional HTS where observing K D 's in the 100 μM to mM range are common (Hajduk and Burns, 2002).…”

“…The SHAPES library is a typical example of the fragment based approach to NMR screening, where the library consists of a small, structurally diverse set of water soluble compounds that correspond to fragments or molecular frameworks of known drugs (Lin et al, 1997;Fejzo et al, 1999;Johnson et al, 2003;Lepre et al, 2002;Moore et al, 2004). A comparable approach to reduce the size of screening libraries is to use NMRbased assays as a secondary screen to validate hits from HTS assays.…”

“…Additionally, NMR may be used to evaluate the physical properties of a chemical lead, measure K D 's (Fielding, 2003), identify ligand binding sites (Roberts, 2000), and determine a co-structure (Clore and Gronenborn, 1994;Cooke, 1997;Kay, 1997;Roberts, 2000). A diverse number of NMR screening approaches have been developed, which include SAR by NMR (Shuker et al, 1996;Hajduk et al, 1997a;Hajduk et al, 1997c;Hajduk et al, 1999b;Johnson et al, 2003), SHAPES (Moore et al, 2004;Lepre et al, 2002;Fejzo et al, 1999), and MS/NMR (Moy et al, 2001). NMR spectroscopy is a relatively insensitive technique requiring higher amounts of material and acquisition time compared to standard methods used in traditional HTS assays.…”