A fragment library was screened against the G protein-coupled histamine H4 receptor (H4R) and the ligand-gated ion channel serotonin 5-HT3A (5-HT3AR). Interestingly, significant overlap was found between H4R and 5-HT3AR hit sets. The data indicates that dual active H4R and 5 HT3AR fragments have a higher complexity than the selective compounds which has important implications for chemical genomics approaches. The results of our fragment-based library screening study illustrate similarities in ligand recognition between H4R and 5-HT3AR and have important consequences for selectivity profiling in ongoing drug discovery efforts on H4R and 5-HT3AR. The affinity profiles of our fragment screening studies furthermore match the chemical properties of the H4R and 5-HT3AR binding sites and can be used to define molecular interaction fingerprints to guide the in silico prediction of protein-ligand interactions and structure
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