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The sphingosine-1-phosphate type 1 (S1P(1)) receptor is a new target in the treatment of auto-immune diseases as evidenced by the recent approval of FTY720 (Fingolimod). The ligand-binding pocket of the S1P(1) receptor has been generally characterised but detailed insight into ligand-specific differences is still lacking. The aim of the current study is to determine differences in ligand-induced S1P(1) receptor activation using an in silico guided site-directed mutagenesis strategy. S1P(1) mutant receptors (modifications of residues Y98(2.57), R120(3.28), F125(3.33)) were probed with a chemically diverse set of S1P(1) agonists (S1P, dihydro-S1P (dhS1P), R-, S- and racemic FTY720-P, VPC24191, SEW2871). Mutation of the R(3.28) residue generally results in a reduction of the potency of all ligands although the synthetic ligands including FTY720-P are less sensitive to these mutations. The Y(2.57)F mutation does not affect the potency of any of the ligands tested, but for all ligands except FTY720-P a significant decrease in potency is observed at the Y(2.57)A mutant. The F(3.33)A mutation significantly decreased the potency of FTY720-P and is detrimental for SEW2871 and VPC24191. The non-aromatic endogenous ligands S1P and dhS1P are less affected by this mutation. Our in silico guided mutagenesis studies identified new molecular determinants of ligand-induced S1P(1) receptor activation: 1) the flexibility of the polar head of the agonist to maintain a tight H-bond network with R(3.28) and 2) the ability of the agonist to make aromatic π-stacking interactions with F(3.33). Interestingly, FTY720-P has both chemical properties and is the only ligand that can efficiently activate the Y(2.57)A mutant.

This review will focus on the construction, refinement, and validation of G-protein-coupled receptor (GPCR) structural models for the purpose of structure-based virtual screening (SBVS) and ligand design. The review will present a comparative analysis of GPCR crystal structures and their implication on GPCR (homology) modeling. The challenges associated with steps along the modeling workflow will be discussed: the use of experimental anchors to steer the modeling procedure, amino acid sequence alignment and template selection, receptor structure refinement, loop modeling, ligand-binding mode prediction, and virtual screening for novel ligands. An overview of several successful structure-based ligand discovery and design studies shows that receptor models, despite structural inaccuracies, can be efficiently used to find novel ligands for GPCRs. Moreover, the recently solved GPCR crystal structures have further increased the opportunities in structure-based ligand discovery for this pharmaceutically important protein family.