SAR-by-NMR approach

Fig. 3 The SAR by NMR approach. Example of a small bidentate molecule designed using this approach. The example shown is for the design of a potent inhibitors of the matrix metalloproteinase MMP3. (a) Docked structures of the identified fragment leads are shown with cyan carbons, whereas the linked compound is shown with green carbon atoms. All structures were experimentally determined by NMR. (b) Chemical structures (and in vitro potencies) of the fragment leads and subsequent high-affinity linked compounds. Adapted from [7]...

The change in the chemical environment of a nucleus at the binding interface of a ligand-protein complex upon binding is likely to induce a change in chemical shift. This effect is used for example as a readout in the SAR by NMR approach to detect binding and thus identify lead molecules (33). Heteronuclear chemical shifts (particularly 13C and 15N) are widely used in such experiments and are detected via HSQC-type (heteronuclear single quantum correlation) experiments. 

Several successful applications of this SAR-by-NMR approach have already been published [32], [37], [38], one of which is shown in Figure 9-11. 

A non-classical, but still rational and structure-based, screening approach was applied by researchers at Abbott Laboratories, utilizing the SAR-by-NMR technique [126, 127] to identify biophysically pTyr mimics for the Lck SH2... 

All the spectroscopic approaches applied for structural characterization of mixtures derive from methods originally developed for screening libraries for their biological activities. They include diffusion-ordered spectroscopy [15-18], relaxation-edited spectroscopy [19], isotope-filtered affinity NMR [20] and SAR-by-NMR [21]. These applications will be discussed in the last part of this chapter. As usually most of the components show very similar molecular weight, their spectroscopic parameters, such as relaxation rates or selfdiffusion coefficients, are not very different and application of these methodologies for chemical characterization is not straightforward. An exception is diffusion-edited spectroscopy, which can be a feasible way to analyze the structure of compounds within a mixture without the need of prior separation. This was the case for the analysis of a mixture of five esters (propyl acetate, butyl acetate, ethyl butyrate, isopropyl butyrate and butyl levulinate) [18]. By the combined use of diffusion-edited NMR and 2-D NMR methods such as Total Correlation Spectroscopy (TOCSY), it was possible to elucidate the structure of the components of this mixture. This strategy was called diffusion encoded spectroscopy DECODES. Another example of combination between diffusion-edited spectroscopy and traditional 2-D NMR experiment is the DOSY-NOESY experiment [22]. The use of these experiments have proven to be useful in the identification of compounds from small split and mix synthetic pools. 

This example underscores the efficiency of SAR-by-NMR and moreover illustrates the fragment-based approach. 

Researchers at Abbott Laboratories used a different approach for discovering high-affinity protein ligands, the structure-activity relationships by nuclear magnetic resonance ( SAR by NMR ) (71). In this method, the relatively large site is divided into two smaller half-sites that are targeted individually by small... 

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