Mechanistic Studies on the Stereoselectivity of the Serotonin 5‐HT_1A Receptor

Abstract

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...

The Molecular Mechanism of P2Y1 Receptor Activation

“…This occurred at 0.8-1.2 msM Dt ime scale.H owever,i nb oth bound antagonists P2Y 1 R*-BPTU and P2Y 1 R-MRS2500, the conformation of Y324 7.53 did not change during the entire simulations.T hese results agree with previous findings [9] showing that Y324 7.53 plays ar ole as as witch, forming acontinuous water channel during GPCR activation.…”

Intracellular passage of Na+in an active state g-protein coupled receptor

“…This channel bridges the extracellular ligand and intracellular G-protein binding sites. Water access from the ligand binding site all the way to the cytoplasmic side of the receptor has previously also been observed in simulations on the A 2A R and 5-HT 1A receptors 24,25 . We show here that the activated receptor state permits the Na + ion to cross the receptor towards the cytoplasmic side, without experiencing any major energy barriers.…”

“…Our simulations show two major conformations of the Y440 7.53 sidechain following the transition -an upward state similar to the conformation observed in the inactive crystal structure (PDB: 3UON; Fig S3B) and a downward configuration, which is also seen in the active crystal structure (PDB: 4MQT; Fig S3A). The formation of a hydrated pathway connecting the receptor ligand and effector binding sites has been reported in previous simulation studies on the A 2A R and 5-HT 1A receptors 24,25 , however the previous reports did not take the presence of a Na + ion into consideration.…”

“…Furthermore, if a G-protein complex with a receptor is preformed before agonist binding, D 2.50 would be readily accessible for protonation from the extracellular side via a hydrated pathway. In this context, it has further been argued that bound agonists, but not antagonists, may sustain the hydrated pathway past the ligand which connects the extracellular space with the Na + ion binding site upon receptor activation 25 .…”

Role of tandospirone, a 5-HT1A receptor partial agonist, in the treatment of central nervous system disorders and the underlying mechanisms

“…Since the crystal structures of 5-HT1B and 5-HT2B receptors have been well studied [ 14 ], a homology model of 5-HT1A receptor using the crystal structure of the 5-HT1B receptor (PDB ID: 4IAQ) was established to explore the structure basis of the stereoselectivity of a prototypical GPCR [ 15 ]. Using molecular interaction fingerprints, it was discovered that the agonist of 5-HT1A receptor could mobilize nearby amino acid residues to form a continuous water channel via molecular switches, while the antagonist of 5-HT1A receptor maintained stabilization in the binding pocket [ 16 ]. Although the accurately targeted site of 5-HT1A receptor by tandospirone is still unknown, it is rational to speculate that as a partial agonist of 5-HT1A receptor, tandospirone may act through forming a continuous water channel by mobilizing nearby amino acid residues.…”