The human olfactory receptor 17-40: requisites for fitting into the binding pocket.

To gain structural insight on the interactions between odorants and the human olfactory receptor, we did homology modelling of the receptor structure, followed by molecular docking simulation with ligands. Molecular dynamics simulation on the structures resulting from docking served to estimate the binding free energy of the various odorant families. A correlation with the odorous properties of the ligands is proposed. We also investigated which residues were involved in the binding of a set of properly synthesised ligands and which were required for fitting inside the binding pocket. Olfactive stimulation of the olfactory receptor with odorous molecules was also investigated, using calcium imaging or electrophysiological recordings

Encoding of Odorants by Olfactory Sensory Neurons

The olfactory system relies on a combinatorial code where a given odorant receptor (OR) detects multiple odorants, and a given odorant is detected by multiple ORs (Malnic, Hirono et al. 1999). Prior attempts to decipher the code have emphasized linking genetic sequence to functional profile, but this approach has led to deorphanization of only ~85 out of ~1200 ORs in mouse (Zhang and Firestein 2007). With such a narrow window onto the combinatorial code, even the deorphaned ORs effectively remain stranded. High throughput calcium imaging of olfactory sensory neurons (OSNs) can provide the missing context. With this method, it is possible to survey the population response patterns while still preserving information on the individual receptive fields that contribute to the ensemble. I have used this technique to gain a more comprehensive view of the combinatorial code. Octanal is an odorant capable of recruiting many OSNs, but how functionally diverse are they? Screening with a panel of odorants made the subdivisions among this large suite of OSNs clear, revealing that nearly half uniquely parse the test panel. Expanding upon this, I show that such rare response patterns can be used like a fingerprint to assess, via physiology, that an OSN expresses a given OR. Population level analysis of the combinatorial code led me to two driving concepts. One is that the OR repertoire, despite its diversity, is nevertheless markedly constrained in its ability to discriminate certain series of odorants. For example, an OSN cannot respond to an alcohol and acid without also responding to an aldehyde. Exploring potential mechanisms, I used designer aldehydes that were trapped in an intermediate polar anchor state. I found that a previously discounted binding mode correlated with the ability of OSNs to selectively respond to aldehydes while excluding alcohols. The other key finding is that odorants can often adopt high energy conformations when activating OSNs. Initially, this was noted for aromatic odorants during a general screen. To probe the phenomenon in greater detail, I used a series of cyclized compounds that mimic rarely assumed states of the flexible tail of octanal. Comparing the activation strength of each analog to that elicited by unconstrained octanal demonstrated extensive co-recognition. This suggests that the flexibility of octanal contributes to its promiscuity in terms of recruiting a high number of OSNs. This study led to the realization that rings could often be treated as merely preserving a particular trajectory of a hydrocarbon backbone. Guided by this concept, I developed new panels with odorants that previously would have been considered discrepant. Hedione is an odorant where a ring imparts specialized geometry that greatly impacts perception. Yet at the OR combinatorial code level, I found that the ring was not critical and flexible but related odorants were still effective. I also demonstrated that OSNs readily accept odorants where an aromatic ring has been substituted with specific alkyl fragments. Thus, aromatic rings too, despite their unique electronics, are sometimes better viewed from a strictly architectural perspective. Using population analysis to identify what the ORs deem the important features of odorants can clarify the trends that sculpt the combinatorial code. This knowledge can help us consolidate seemingly broad receptive fields to better understand what information the OR repertoire extracts from the external chemical environment

Characterisation, antioxidant properties and cytoprotective investigation of Zanthoxylum zanthoxyloides root-bark in oxidative stressed promyelocytic leukaemia cells

There is great interest in traditional or folk medicines in order to help with the discovery and development of potentially new pharmaceutics which have clinical benefits to man. Many of these traditional medicines are derived from medicinal plants which have been shown to contain a multitude of chemicals that have potent natural antioxidant properties. The chemical composition (metabolites), characterisation, antioxidant properties and cytoprotective effects to oxidative stress of Zanthoxylum zanthoxyloides (ZZ) root-bark extract obtained from different seasonal conditions, namely: winter, spring, summer and autumn bought from an African store and during one annual collection, were investigated in this thesis. ZZ root-bark was prepared in in two solvents (ethanol and water) and three methods of extraction (Aq decoction and maceration as well as ethanolic maceration). The extracts were investigated using different methods such as moisture content analysis, percentage insoluble fraction, spectrocolorimetric measurements, ash content analysis, analysis of carbon, sulphur, nitrogen, hydrogen and oxygen analysis, gas chromatography-mass spectroscopy (GC-MS), ultra-violet-visible spectroscopy (UV-VIS), Fourier-transform infra-red spectroscopy (FT-IR), qualitative and quantitative phytochemical analyses. Its antioxidative effects was investigated by assessing the plant extract’s ability to scavenge or react with a range of different free radicals such as: 2,2-diphenyl-1-picrylhydrazyl radical (DPPH), hydroxyl radical (●OH), singlet oxygen radical (1O2), nitric oxide radical (NO●), 2,2-azino-bis(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS●+), metal ion, ferric reducing antioxidant power assay (FRAP) and reducing power assay. Lipopolysaccharide (LPS) and H2O2 were used to induce oxidative stress in human leukemic cells (U937 and HL60), and the ZZ extract was used to determine any potential cytoprotective effects to these oxidative insults. The result presented in this thesis showed that the moisture content of ZZ root-bark extract for winter, summer, spring and autumn was between 6.75 – 8.07% and this is within the acceptable moisture content percentage (5 – 8%). A statistically significant difference of *P<0.5 (winter vs spring), ***P<0.001 (spring vs summer) and ****P<0.0001 (winter vs summer) was observed among these seasons. The percentage insoluble fraction of this extract, in both solvents, was about 90% for these seasonal conditions with no statistically significant difference among them. The percentage ash content was between 6.9 – 8.3% for these harvest seasons, with statistically significant difference of *P<0.5 (winter vs spring) and **P<0.01 (winter vs summer), and this is within the acceptable range (5 – 40%). ICP-MS analysis of this extract confirms the presence of calcium, manganese, gallium, strontium, barium, lanthanum and cerium for all extracts from different seasons. GC-MS analysis of ZZ confirms the presence of many metabolites such as alkyl amide, lipids, coumarin, alkaloids, phenolics and triterpenes from all seasons. UV-VIS spectroscopy analysis further confirmed the presence of flavonoids for all seasons. Physico-chemical quantification analyses also confirmed the presence of many of these constituents in the extract. Percentage CHNS-O was between 43 – 52 % for carbon, 0 – 0.21 % for nitrogen, 4 – 12 % for hydrogen and 35 – 41 % for oxygen. However, sulphur was not present in all seasons. The ZZ extract also showed a great ability to scavenge free radicals such as DPPH● (IC50 = 30 μg/ml), ●OH (IC50 = 0.08 mg/ml), H2O2 (IC50 = 0.08 mg/ml), NO● (IC50 = 0.20 mg/ml) 1O2 (IC50 = 0.16 mg/ml) ABTS●+ (IC50 = 0.23 mg/ml) and metal ion (IC50 = 0.11 mg/ml) by accepting hydrogen or electron but showed a weak FRAP and reducing power ability. Finally, the extract showed it had cytoprotective effect against lipopolysaccharide and hydrogen peroxide-induced oxidative stress leading to cell death in U937 and HL60 leukemic cells. A more detailed characterisation showed that the ZZ extract was able to statistically protect against oxidative stress-induced cell death caused by either apoptosis or necrosis. In conclusion, ZZ extract possesses many phytochemical compounds, many of which have antioxidants properties regardless of their harvest seasons. Findings from this thesis confirmed the potential health benefits of ZZ root-bark and could be valuable for pharmaceutical and nutraceutical industries in using it to reveal new sources of natural antioxidant for therapeutic drugs