Auxin (Indole-3-acetic acid; IAA) can be considered one of the most important hormones in plant development as it coordinates plant development through transcriptional regulation. For years the principal auxin receptor was sought and only relatively recently was it identified as an F-box protein known as TIR1, with five homologues; the auxin F-Box proteins (AFB1–5). The elucidation of a crystallographic structure elegantly demonstrated IAA’s integral role in forming a ternary complex between auxin F-box proteins and Aux/IAA proteins, revealing the mechanism of auxin perception. An exact chemical description of an auxin has been pursued for decades and researchers have always faced the challenge of factoring in the complex nature of multiple auxin-receptor classes, transport and metabolism. My project aimed to develop a better understanding of auxin chemical specificity at the receptor level, focusing on TIR1 and one of its most distantly related homologues, AFB5. We employed a structure activity relationship study with a rational selection of compounds and have defined a pharmacophore for auxin activity for the TIR1 receptor. The thesis also describes a receptor-led, in silico rational drug design approach in which we replaced the carboxylic acid moiety with a tetrazole, giving a novel compound that demonstrated auxin-like activity both in vitro and in vivo. Furthermore this bioisosteric replacement serendipitously demonstrated a novel selectivity for TIR1, with no activity against AFB5. Preliminary in silico docking studies of the TIR1 binding site could not discern between active and in active compounds generating many false positive results, leading us to develop TomoDock; a novel in silico docking approach to study the entire TIR1 receptor binding pocket geometries. Results from TomoDock suggest that binding is a two phase process with active ligands firstly engaging with a niche, which orients them, allowing passage past and molecular filter region before interacting with the binding site. This process contributes to the mechanism of compound selection by the TIR1 pocket receptor. A range of multidisciplinary approaches utilised in this project have allowed us to investigate and report many new insights on the mechanism of auxin perception. Such rational approaches may also be used in other drug discovery programmes alike to help researchers discern compound perception and selectivity.
| Identifer | oai:union.ndltd.org:bl.uk/oai:ethos.bl.uk:714949 |
| Date | January 2016 |
| Creators | Quareshy, Mussa |
| Publisher | University of Warwick |
| Source Sets | Ethos UK |
| Detected Language | English |
| Type | Electronic Thesis or Dissertation |
| Source | http://wrap.warwick.ac.uk/89114/ |
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