G-protein-coupled receptors (GPCRs) are involved in a wide range of physiological processes, and they have attracted considerable attention as important targets for developing new medicines. A central and largely unresolved question in drug discovery, which is especially relevant to GPCRs, concerns ligand selectivity: Why do certain molecules act as activators (agonists) whereas others, with nearly identical structures, act as blockers (antagonists) of GPCRs? To address this question, we employed all-atom, long-timescale molecular dynamics simulations to investigate how two diastereomers (epimers) of dihydrofuroaporphine bind to the serotonin 5-HT 1A receptor and exert opposite effects. By using molecular interaction fingerprints, we discovered that the agonist could mobilize nearby amino acid residues to act as molecular switches for the formation of a continuous water channel. In contrast, the antagonist epimer remained firmly stabilized in the binding pocket.The growing number of crystal structures and related computer simulations of G-protein-coupled receptors (GPCRs) have resolved a number of structural key features in the activation process of GPCRs, including ligand-binding specificity, side-chain molecular switches, rearrangement of transmembrane helices, and formation of internal water channels. [1][2][3][4][5][6][7][8][9][10] In spite of this progress, many important mechanistic principles of GPCR-mediated signalling remain poorly understood at the molecular level. An example is ligand stereoselectivity, which is a central concern in drug discovery since it substantially influences the efficacy, efficiency, and metabolic properties of drug candidates. [11,12] Molecular dynamics could be of great help towards addressing such unresolved issues. [9,10] In this work, we used all-atom, long-timescale molecular dynamics (MD) simulations to investigate the ligand stereoselectivity of the serotonin 5-HT 1A receptor and determine how the stereochemical arrangement of a single methyl group at a chiral carbon atom determines whether the ligand acts as an agonist or an antagonist.For a pair of dihydrofuroaporphine epimers, functional assays have identified one epimer to be a full agonist and the other to be a full antagonist of the serotonin 5-HT 1A receptor. [13,14] The configuration of a single methyl group is the only structural difference between this pair of diastereomers, and it results in different functional properties as ligands for the receptor (Scheme 1).To explain the structural basis of this stereoselectivity of a prototypical GPCR, we first built a homology model of the 5-HT 1A receptor by using the crystal structure of the 5-HT 1B receptor (PDB ID: 4IAQ) [15] for an agonist-bound receptor structure template and that of the M3 muscarinic receptor (PDB ID: 4U15) [16] for an antagonist-bound receptor structure template. Interestingly, the superimposed crystal structures of the two receptors are almost identical ( Figure S1 in the Supporting Information), with an RMSD of less than 1.5 for the TM backbone...