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Browsing by Subject "receptor activation"

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  • Karhu, Lasse (2012)
    The orexinergic system is a central regulator for sleep-wake rhythm and energy homeostasis. Dysfunction of the system is at least one of the reasons behind narcolepsy, in addition to which insomnia, obesity and certain cancers could be treated by targeting orexin receptors. The orexin system in human comprises two receptor subtypes, orexin receptor 1 and 2 (OX₁R and OX₂R respectively) as well as two cognate ligands, peptides orexin-A and -B. In this study the focus is on OX₁R and orexin-A. The aims of the study are (1) to propose a binding mode for orexin-A to OX₁R and (2) to understand the molecular interactions of OX₁R leading to receptor activation. I order to create 3D molecular models of OX₁R, a sequence alignment of the eight G proteincoupled receptors (GPCRs) that have been crystallized up to date was first generated by ClustalX and adjusted based on the superimposition by SYBYL-X. Structurally conserved regions were deduced from the alignment and used to add the orexin receptors. Five different models built with MODELLER were selected for their large binding cavity among a large pool of models. These models were constructed based on the chemokine receptor 4 (PDB Id:3ODU), as such and a modified version where TM3 was moved by 1 Å further from the center of the binding cavity, from the β₂-adrenoceptor (PDB Id: 2RH1) and from the adenosine receptor A2A (PDB Id: 2YD0), as such and with rotamer changes to few binding site residues. Orexin-A with straight conformation found by NMR (PDB Id:1WSO) was docked to these models using ZDOCK and RDOCK. In addition, an in-house docking protocol was implemented, but could not be validated. Docking poses were scored by purpose built knowledge based scoring function and clustered. High scoring clusters were then used to converge to three different binding modes. As a result, we suggest that the binding site of OX₁R consists of two hydrophobic walls, one from TM3 and TM5, the other from TM6 and TM7. Binding modes include a hydrogen bond network between the ligand and especially binding site residues Gln1263.32, Thr2235.46, Asn3186.55, Lys3216.58 and Tyr3117.43. Based on the binding modes, it is suggested that the OX₁R is activated by similar binding site contraction as β-adrenoceptors and adenosine A2A. The contraction in could result from the hydrogen bonds between ligand, Gln1263.32, Thr2235.46 and Asn3186.55. The hydrogen bonding of Thr2235.46 can also disrupt interactions between TM5 and TM3, an interaction which is identified as an important factor in keeping the receptor in the inactive state. The role of other ligand residues would be to direct ligand binding and keep the ligand in the helical conformation.
  • Vartiainen, Pyry (2023)
    Orexins (hypocretins) are two neuropeptides, orexin-A (OX-A) and orexin-B (OX-B), produced by a neuron subpopulation in the mammalian hypothalamus. They are natural substrates of two G-protein-coupled receptors (GPCRs), orexin receptor 1 (OX1R) and orexin receptor 2 (OX2R), respectively. Orexin receptors are expressed widely in the central nervous system. Orexin peptides and receptors were originally discovered in 1998 and have been extensively researched ever since. Maintaining a steady state of wakefulness has been identified as one main physiological function of orexinergic signalling, and loss of orexinergic neurons in the hypothalamus has been linked to narcolepsy. Over the past decade orexin receptor antagonists have been developed for treatment of insomnia – suvorexant as the first one, approved for clinical use in 2014. Orexin receptor agonists remain under development for treatment of narcolepsy as one potential therapeutical indication, with no clinical applications yet approved. Orexin receptor activation by small-molecule agonists has proven a challenge not yet conclusively resolved. The aim of this study was to validate a novel scaffold for orexin receptor agonists from compounds identified as orexin receptor agonists in previous studies. Total of ten compounds were designed for synthesis, three of which were successfully synthesized. These three compounds exhibited very low orexinergic activity (0.06–1.36% and 2.33–5.19% response of full activation for OX1R and OX2R, respectively). After activity testing retrospective modelling of the receptor binding of the synthesized and designed compounds was implemented computationally by structure-based molecular docking to the recently discovered (2021) crystal structure of OX2R in complex with bound small-molecule agonist 3′-(N-(3-(2-(2-(2H-1,2,3-triazol-2-yl)benzamido)ethyl)phenyl)sulfamoyl)-4′-methoxy-N,N-dimethyl-[1,1′-biphenyl]-3-carboxamide. Some of the key interactions known as crucial for receptor activation, such as hydrogen bonds with glutamine Q1343.32, were found possible for some of the synthesized and designed compounds. This may in part explain the orexinergic activity, however very low, measured for the synthesized compounds. Low activity of the synthesized compounds may be a result of low binding since their binding was not tested in this study. Interactions between the synthesized compounds and OX2R predicted by molecular modelling are consistent with the low measured activity of the compounds, and alternative, more optimal chemical scaffolds for orexin receptor activation could be searched in future studies.