Design, Synthesis and Pharmacological Evaluation of 5-Hydroxytryptamine_1aReceptor Ligands to Explore the Three-Dimensional Structure of the Receptor

Abstract

In this work, we evaluate the structural differences of transmembrane helix 3 in rhodopsin and the 5-hydroxytryptamine 1A (5-HT 1A ) receptor caused by their different amino acid sequence. Molecular dynamics simulations of helix 3 in the 5-HT 1A receptor tends to bend toward helix 5, in sharp contrast to helix 3 in rhodopsin, which is properly located within the position observed in the crystal structure. The relocation of the central helix 3 in the helical bundle facilitates the experimentally derived interactions between the neurotransmitters and the Asp residue in helix 3 and the Ser/Thr residues in helix 5. The different amino acid sequence that forms helix 3 in rhodopsin (basically the conserved Gly 3.36 Glu 3.37 motif in the opsin family) and the 5-HT 1A receptor (the conserved Cys 3.36 Thr 3.37 motif in the neurotransmitter family) produces these structural divergences. These structural differences were experimentally checked by designing and testing ligands that contain comparable functional groups but at different interatomic distance. We have estimated the position of helix 3 relative to the other helices by systematically changing the distance between the functional groups of the ligands (1 and 2) that interact with the residues in the receptor. Thus, ligand 1 optimally interacts with a model of the 5-HT 1A receptor that matches rhodopsin template, whereas ligand 2 optimally interacts with a model that possesses the proposed conformation of helix 3. The lack of affinity of 1 (K i Ͼ 10,000 nM) and the high affinity of 2 (K i ϭ 24 nM) for the 5-HT 1A receptor binding sites, provide experimental support to the proposed structural divergences of helix 3 between the 5-HT 1A receptor and rhodopsin.

Heavier‐than‐air flying machines are impossible

“…A survey of recent, GPCR modelling‐related literature revealed a series of flaws: Total neglect of loops and the IV–V hairpin [27–30]; Modelling loops based on data for individual loops obtained from nuclear magnetic resonance experiments or from sequence similarity with another PDB file [31–34]; …”

Influence of the g− conformation of Ser and Thr on the structure of transmembrane helices

“…In addition to its role in modulating the structure of TMs, Ser and Thr residues are also reported to play key roles in preserving the overall structure of membrane proteins (Lopez-Rodriguez et al, 2002), stabilizing the interactions between TMs (Dawson et al, 2002;Eilers et al, 2002), and regulating protein function (Munshi et al, 2003;Jongejan et al, 2005;Pellissier et al, 2009). In addition, mutations involving polar residues in TM segments are often associated with protein malfunction (Partridge et al, 2004;Smit et al, 2007), being the most common disease-causing mutations in membrane proteins (Joh et al, 2008).…”

Pharmacological Differences between Human and Guinea Pig Histamine H1 Receptors: Asn84 (2.61) as Key Residue within an Additional Binding Pocket in the H1 Receptor

“…Water molecules present in the rhodopsin structure were retained, and their heavy atoms were kept fixed during all minimizations and molecular dynamic runs. The position of TM3 was manually changed with regard to the rhodopsin structure to avoid a clash between the top of TM3 and TM2 (Lopez-Rodriguez et al, 2002). Given the presence of the H 1 R-specific Trp 158 (4.56), TM3 could not be put into the position as found by molecular modeling studies on the 5HT 1A receptor.…”