Dissertation

A Comparative Analysis of the Principles behind α7 Nicotinic Acetylcholine Receptor Function

Gulsevin, Alican

2017

Overview

Silent agonists are α7 nicotinic acetylcholine receptor ligands that do not evoke a response larger than 10% of the acetylcholine control but put the receptor into a desensitized state (Ds). They show robust potentiated responses when co-applied with a type-II positive allosteric modulator. Homology modeling, molecular dynamics, molecular docking, binding free energy calculations and voltage clamp electrophysiology were used to determine the roots of silent agonism at the α7 nAChR. α7 nAChR is a therapeutic target for several diseases related to its activity as an ion channel and due to its non-ionotropic modulatory role in immune cells. Despite the therapeutic importance of the α7 receptor, governing principles behind the mode of action of the α7 receptor silent agonists are not clear because experimental studies cannot capture the events happening at a shorter time scale than the channel opening time, and computational studies of the receptor are held down by the lack of a high resolution receptor structure and the highly dynamical nature of the protein. Therefore, the use of experimental and computational methods in conjunction is the best strategy to compensate for the disadvantages of either method. Homology modeling, docking, and molecular dynamics studies with the WT α7 nAChR and the Q57T, W55V, W55Y, Y93C, and C190A mutants showed that local structural changes can have global effects unpredictable by simple computational approaches. These effects include changes in overall receptor geometry, symmetry, and the location of alternative binding sites on the receptor. Molecular descriptors from quantum mechanics calculations, molecular mechanics based binding energy calculations, and structural elements of the receptor were correlated with silent agonist behavior for a group of α7 ligands. Some of these correlates from in silico analyses were confirmed by voltage clamp experiments that showed silent agonism has an element directly related to the binding configuration of the ligand molecules at the orthosteric site, but also has an element independent of the traditional agonism because changes that abolished agonist activity did not necessarily affect silent agonism. Overall, a systematic analysis of the current literature, 7 receptor analogs and mutants, and α7 silent agonists was done to identify the important factors in modeling α7 nAChR and roots of silent agonism.

• Publisher: ProQuest Dissertations & Theses
• Subject: Biochemistry / Bioinformatics / Molecular biology
• ISBN: 9798691292873