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Fragment-Based Lead Discovery by NMR

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NMR is a powerful tool for fragment-based lead discovery comprising robust techniques for screening, core elaboration and fragment linking as well as 3D protein-ligand structure determination. Utilizing a direct binding assay that solely contains protein and ligand, NMR detects loose fragment binders with unparalleled sensitivity and robustness even in the millimolar affinity range. Excellent research during the last ten years established protein- and ligand- detected NMR screening assays for soluble proteins below and above 50 kD, respectively. Site-specific methods, such as spin-label perturbation and InterLigand- NOE (ILOE) NMR screening allow one to selectively detect fragment binding to allosteric or adjacent second sites. Target-immobilized NMR screening (TINS) reduces protein consumption and potentially enables screening of membrane proteins.

NMR supports fragment-to-lead optimization through chemical shift perturbation SAR maps and fragment linking through ILOE information at timely throughput of >= 20 compounds / day. 3D protein-ligand structures for structure- based design require more time (> 1 month / compound) and thus are limited to few representative ligands.

Further research is required to make such NMR techniques amenable to proteins with poor expression yield, low solubility, sole expression in mammalian systems and ultimately to membrane proteins. Some of these bottlenecks are circumvented by integrating NMR into HTS, computational docking and cocrystallization platforms, which is an important future direction.

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Keywords: Interligand noe-detected assays; fragment libraries; molecular weight (mw) analysis; protein-detected nmr assays; water-logsy

Document Type: Research Article

Publication date: March 1, 2007

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