Small and colorful stones make beautiful mosaics: fragment-based chemogenomics

• Published in: Drug discovery today Vol. 18; no. 7-8; pp. 323 - 330
• Main Authors: de Graaf, Chris, Vischer, Henry F., de Kloe, Gerdien E., Kooistra, Albert J., Nijmeijer, Saskia, Kuijer, Martien, Verheij, Mark H.P., England, Paul J., van Muijlwijk-Koezen, Jacqueline E., Leurs, Rob, de Esch, Iwan J.P.
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 01.04.2013
• Subjects: Binding Sites; Cyclic AMP-Dependent Protein Kinase Catalytic Subunits - chemistry; Cyclic AMP-Dependent Protein Kinase Catalytic Subunits - metabolism; Drug Discovery; HEK293 Cells; Humans; Ligands; Pharmaceutical Preparations - metabolism; Protein Binding; Receptors, G-Protein-Coupled - chemistry; Receptors, G-Protein-Coupled - metabolism; Receptors, Serotonin, 5-HT3 - chemistry; Receptors, Serotonin, 5-HT3 - metabolism; Small Molecule Libraries
• ISSN: 1359-6446; 1878-5832
• DOI: 10.1016/j.drudis.2012.12.003

[Display omitted] ► Fragment screening represents a high-resolution chemogenomics approach. ► Probing protein-binding sites with fragments results in new molecular insights. ► Affinity cliffs and molecular selectivity switches guide hit fragment optimization. Smaller stones with a wide variety of colors make a higher resolution mosaic. In much the same way, smaller chemical entities that are structurally diverse are better able to interrogate protein binding sites. This feature article describes the construction of a diverse fragment library and an analysis of the screening of six representative protein targets belonging to three diverse target classes (G protein-coupled receptors ADRB2, H1R, H3R, and H4R, the ligand-gated ion channel 5-HT3R, and the kinase PKA) using chemogenomics approaches. The integration of experimentally determined bioaffinity profiles across related and unrelated protein targets and chemogenomics analysis of fragment binding and protein structure allow the identification of: (i) unexpected similarities and differences in ligand binding properties, and (ii) subtle ligand affinity and selectivity cliffs. With a wealth of fragment screening data being generated in industry and academia, such approaches will contribute to a more detailed structural understanding of ligand–protein interactions.