Fragment library screening reveals remarkable similarities between the G protein-coupled receptor histamine H4 and the ion channel serotonin 5-HT3A

Abstract

Graphical abstract

Cell-based and virtual fragment screening for adrenergic α2C receptor agonists

“…This active rate, although much higher than under conventional HTS settings, is comparable to those reported for GPCRs using diverse assays as TINS, SPR, 10 intact cell binding 14 and conventional biochemical screening. 16,17 24% of confirmed hits were found to prefer α 2C over an unrelated target, and 76% of these displayed significant activity in a biochemical assay as well. In virtual screening 2 out of the 16 hits were identified in the top 1% of the fragment library providing moderate enrichment but useful structural information on the hits.…”

“…Apart from these successful examples, where challenging targetspecific preparations were crucial for the actual screening process, some experiences with more generic assay formats for probing membrane proteins have been reported as well. [15][16][17] Often, drug discovery programs require ligands that stimulate or potentiate membrane receptors. Although the understanding on the molecular basis of GPCR function increased tremendously in the last years, 18 the structural basis of distinct biological responses is still poorly understood.…”

Fragment-based lead discovery on G-protein-coupled receptors

“…Screening at 1 mM concentration resulted in 9% hit rate, followed by rapid hit expansion on druglike derivatives of fragment hits. Fragment screening of several histamine receptors subtypes and adrenergic β 2 receptor using radioligand has been reported (55,56). The somewhat low test concentration in the binding assays (10 µM) was justified by the 0.4-6% hit rate on the particular library.…”

Structure-based virtual screening for fragment-like ligands of the G protein-coupled histamine H4receptor

“…11,14,15 Biochemical and biophysical fragment screening studies of small chemical libraries (circa 25-1010 compounds) against different GPCRs have been reported with 0.4-14% hit rates yielding several new chemical starting points for fragment-based GPCR ligand optimization. 14,[16][17][18][19][20][21][22] So far only few experimental screens of the same fragment library against multiple GPCR targets have been reported 14,16 that can provide information about the molecular determinants of GPCR-ligand selectivity by fragment-based chemogenomics analyses. 14,23 Virtual fragment screening approaches, the in silico prediction of fragment binding to protein binding sites that has the potential to explore protein-ligand space more extensively, have been successfully applied to identify new fragment-like ligands for several GPCR targets, with 20-73% hit rates (% of experimentally tested in silico hits with detectable binding affinity).…”

“…ii) the retrospective validation, comparison, and optimization of different virtual screening approaches based on a training set containing not only known H 4 R fragmentlike ligands but also experimentally validated inactive fragments. 13,17 The IFP scoring method has been shown to outperform energy-based scoring methods in previous GPCR structure-based virtual (fragment) screening studies 36,73,74 and enable the identification of new chemical ligand scaffolds. 18,24,25 Optimal structure-based virtual screening approaches identified in the current study will therefore be compared with two-dimensional (2D) and three dimensional (3D) ligand-based virtual screening methods.…”