Selective Activation of GPCRs: Molecular Dynamics Shows Siponimod Binds but Fails To Activate S1PR2, Unlike S1PR1

G protein-coupled receptors (GPCRs) are central to drug
discovery,
accounting for nearly 40% of approved pharmaceuticals due to their
regulatory role in diverse physiological processes. Given the high
structural similarity among homologues, achieving receptor selectivity
while minimizing off-target effects remains a major challenge in designing
drugs that target GPCRs. Sphingosine-1-phosphate receptors (S1PRs),
comprising five subtypes, are therapeutically important GPCRs critical
for immune and cardiovascular functions. Siponimod, an FDA-approved
drug for multiple sclerosis, selectively modulates S1PR1 over S1PR2,
unlike earlier S1PR modulators. However, the molecular basis for this
selectivity is unclear, as cellular and biochemical assays provide
limited insights. In this study, we used long-time-scale molecular
dynamics simulations to investigate how S1P and Siponimod binding
affects the structural dynamics of S1PR1 and S1PR2. Both ligands exhibited
strong active site binding in both receptors. Crucially, while S1P
and Siponimod induced similar activation-linked conformational changes
in S1PR1, Siponimod failed to trigger these rearrangements in S1PR2.
Specifically, Siponimod binding to S1PR2 led to altered side-chain
dynamics of key TM7 residues (viz., Y7.37, F7.38, F7.39) and a drift of transmembrane helix 6 (TM6) toward
orientations observed in the inactive state. These unique structural
features differentiate Siponimod’s behavior from S1P and explain
its inability to modulate S1PR2. Our findings elucidate molecular
determinants of Siponimod’s selectivity toward S1PR1 and highlight
these residues as potential differentiators for selective modulator
design. This study demonstrates how structural and dynamic insights
from atomistic simulations aid rational drug design for targets with
high homology.