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

Understanding drug selectivity is crucial for designing effective medications that target specific proteins while minimizing off-target interactions, thus optimizing therapeutic outcomes. Biochemical and cellular assays provide functional insights but often lack detailed molecular understanding of selectivity in large families of similar proteins. In such cases, computational studies can complement experimental approaches to fill gaps in understanding drug selectivity. In this study, Molecular Dynamics (MD) simulation methods have been used to examine the selective modulation of sphingosine-1-phosphate receptor 1 (S1PR1) over S1PR2 by Siponimod, an FDA-approved drug for Multiple Sclerosis. Both S1PR1 and S1PR2 belong to the same sub-family of G Protein-Coupled Receptors (GPCRs). Contrary to the previous hypothesis based on molecular docking, MD simulations showed that Siponimod can bind to S1PR2 with an in silico -determined affinity comparable to that of S1PR1. Comparing the dynamics of Siponimod-bound S1PR2 with S1P-bound S1PR2 revealed that the transmission switches necessary for downstream biological activity are activated by S1P but not by Siponimod, whereas both S1P and Siponimod activate those transmission switches in S1PR1. A few crucial residues in S1PR2 were also identified that can be leveraged to optimize molecules to bind selectively to S1PR1 over S1PR2. Through our study, we showed that in silico approaches can help in understanding the ligand-induced structural changes and aid in developing and optimizing drugs for GPCRs, the most abundant class of membrane proteins in the human genome and the largest family of membrane receptors targeted by approved drugs.