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Crystal Structure-Based Virtual Screening for Fragment-like Ligands of the Human Histamine H1 Receptor

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† Leiden/Amsterdam Center for Drug Research (LACDR), Division of Medicinal Chemistry, Faculty of Science, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
‡ Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, GAC-1200, La Jolla, California 92037, United States
§ Human Receptor Crystallography Project, ERATO, Japan Science and Technology Agency, Yoshidakonoe-cho, Sakyo-ku, Kyoto 606-8501, Japan
∥ Graduate School of Pharmaceutical Sciences, Kyushu University, 3-1-1 Maidashi, Higashi-ku, Fukuoka 812-8582, Japan
⊥ Division of Molecular Biosciences, Membrane Protein Crystallography Group, Imperial College, London SW7 2AZ, U.K.
# Diamond Light Source, Harwell Science and Innovation Campus, Chilton, Didcot, Oxfordshire OX11 0DE, U.K.
× Department of Cell Biology, Graduate School of Medicine, Kyoto University, Yoshidakonoe-cho, Sakyo-Ku, Kyoto 606-8501, Japan
Phone: +31 20 5987600. Fax: +31 20 5987610. E-mail: [email protected]
Cite this: J. Med. Chem. 2011, 54, 23, 8195–8206
Publication Date (Web):October 18, 2011
https://doi.org/10.1021/jm2011589
Copyright © 2011 American Chemical Society
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    Abstract

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    The recent crystal structure determinations of druggable class A G protein-coupled receptors (GPCRs) have opened up excellent opportunities in structure-based ligand discovery for this pharmaceutically important protein family. We have developed and validated a customized structure-based virtual fragment screening protocol against the recently determined human histamine H1 receptor (H1R) crystal structure. The method combines molecular docking simulations with a protein–ligand interaction fingerprint (IFP) scoring method. The optimized in silico screening approach was successfully applied to identify a chemically diverse set of novel fragment-like (≤22 heavy atoms) H1R ligands with an exceptionally high hit rate of 73%. Of the 26 tested fragments, 19 compounds had affinities ranging from 10 μM to 6 nM. The current study shows the potential of in silico screening against GPCR crystal structures to explore novel, fragment-like GPCR ligand space.

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    Additional analysis results of the retrospective and prospective virtual screening studies, H1R, H3R, and H4R radioligand displacement curves, and InsP accumulation barplots; a zipped file containing molecular structures of ligand test set (SMILES) and receptor mol2 coordinates (H1R crystal structure), PLANTS docking conf(iguration) file, reference IFP bit-strings, and cavity coordinates used for IFP calculations. This material is available free of charge via the Internet at http://pubs.acs.org.

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