Discovery of Fragment Molecules That Bind the Human Peroxiredoxin 5 Active Site

The search for protein ligands is a crucial step in the inhibitor design process. Fragment screening represents an interesting method to rapidly find lead molecules, as it enables the exploration of a larger portion of the chemical space with a smaller number of compounds as compared to screening based on drug-sized molecules. Moreover, fragment screening usually leads to hit molecules that form few but optimal interactions with the target, thus displaying high ligand efficiencies. Here we report the screening of a homemade library composed of 200 highly diverse fragments against the human Peroxiredoxin 5 protein. Peroxiredoxins compose a family of peroxidases that share the ability to reduce peroxides through a conserved cysteine. The three-dimensional structures of these enzymes ubiquitously found throughout evolution have been extensively studied, however, their biological functions are still not well understood and to date few inhibitors have been discovered against these enzymes. Six fragments from the library were shown to bind to the Peroxiredoxin 5 active site and ligand-induced chemical shift changes were used to drive the docking of these small molecules into the protein structure. The orientation of the fragments in the binding pocket was confirmed by the study of fragment homologues, highlighting the role of hydroxyl functions that hang the ligands to the Peroxiredoxin 5 protein. Among the hit fragments, the small catechol molecule was shown to significantly inhibit Peroxiredoxin 5 activity in a thioredoxin peroxidase assay. This study reports novel data about the ligand-Peroxiredoxin interactions that will help considerably the development of potential Peroxiredoxin inhibitors

1D NMR WaterLOGSY as an efficient method for fragment-based lead discovery

WaterLOGSY is a sensitive ligand-observed NMR experiment for detection of interaction between a ligand and a protein and is now well-established as a screening technique for fragment-based lead discovery. Here we develop and assess a protocol to derive ligand epitope mapping from WaterLOGSY data and demonstrate its general applicability in studies of fragment-sized ligands binding to six different proteins (glycogen phosphorylase, protein peroxiredoxin 5, Bcl-xL, Mcl-1, HSP90, and human serum albumin). We compare the WaterLOGSY results to those obtained from the more widely used saturation transfer difference experiments and to the 3D structures of the complexes when available. In addition, we evaluate the impact of ligand labile protons on the WaterLOGSY data. Our results demonstrate that the WaterLOGSY experiment can be used as an additional confirmation of the binding mode of a ligand to a protein

Evolution et nouvelles tendances dans les sciences analytiques pour le domaine pharmaceutique

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NMR for Chemical Biology and Drug Discovery

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NMR approaches in fragment-based drug design

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Le criblage de fragments

Le criblage de molécules fragments a obtenu un succès incontestable ces dix dernières années pour la conception de médicaments et apparaît aujourd’hui comme une des voies incontournables pour générer des candidats dans le cas de cibles thérapeutiques ambitieuses et difficiles. Dans cette revue, les principaux concepts et les raisons du succès de la méthode des fragments sont rappelés, et les techniques et stratégies utilisées dans cette approche sont discutées

NMR for fragment-based drug design

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Identifying Protein Allosteric Transitions for Drug Discovery with 1D NMR

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Overview of liquid-NMR approaches for fragment-based lead discovery

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