Health, Medicine, Nursing Thesis Writing Assignment. (Thesis Sample)

IN SILICO DESIGN AND SCREENING OF POTENTIAL CHEMICAL PROBE DERIVED FROM ZINC NATURAL DERIVATE DATABASE AS SPECIFIC DETECTOR OF THERMOSTABLE PORCINE PEPTIDE: APPLICATION FOR RAPID HALAL AUTHENTICATION

ABSTRACT
Introduction: The need for rapid Halal authentication procedure has become an international concern due to the increase in meat adulteration cases. To date, halal authentication methods are mostly expensive, time-consuming and need modern equipment and expert personnel to run the test which will limit the methods' reliability to be used as routine authentication procedure. Objectives: This study is aimed to design and evaluate potential chemical probe(s) specific to detect a thermo-stable porcine peptide (named AQ1) either in raw or thermally processed food products in silico, was consistently detected in contaminated-pork meat products and processed pork that was derived from serum albumin protein. Methodology: Probe design was carried out in silico, starting by solving the 3D peptide structure via homology modelling using I-Tasser software. By using LigandScout software, pharmacophore query was generated for the AQ1 peptide template to run virtual screening procedures to retrieve a number of potential chemical probe(s) from Zinc databases. Specific filters (toxicity and Lipinski rule of five filters) from ChemBioserver were applied to minimise the number of hits. Lastly, docking of potential was performed using AutoDock Vina software to predict their binding properties and to selectively choose top 10 potential lead compounds as probe candidate(s). Result: Findings showed 11 possible hits derived from Zinc natural derivatives database that can be retrieved from the webserver. Upon binding, compound no 8680732 presented highest binding affinity to the AQ1 peptide at -5.2 kcal/mol. The compound showed hydrogen bonding with asparagine at residue 5A at 2.14 Armstrong, which is considered as moderately strong hydrogen bonding. Compound no 478771 the second highest binding affinity of -4.8 kcal\mol. Discussion: This study highlight the ability of in silico methods to design potential probes for the detection of specific porcine peptide. The data obtained from the study showed a moderately high binding property of the ligands from Zinc natural derivatives software, which indicated the possibilities of the compound to be developed as specific chemical probe for halal authentication procedure compare to other 11 compounds. Nevertheless, further study is needed to test different software that may produce compounds with better binding possibilities to the AQ1 peptide. Conclusion: no 868072 showed the best binding potential to the AQ1 peptide that highlight its potential to be developed as specific chemical probe for halal authentication procedure.
Keywords: AQ1 peptide, chemical probe design, in silico
CHAPTER ONE: INTRODUCTION
1.1 Background
Halal is an Arabic word that simply means anything that is lawful or permissible (Riaz 1996). When the term is used in the context of meat production and consumption, such meat must be extracted from particular animals that are slaughtered in accordance with the provisions in the Hadith and Quran (Fuseini et al., 2017). In the Muslim community, it is generally agreed that for meat to be acceptable for consumption, the associated animal should be acceptable for Halal, especially, that such animals should be well and fit at the time of slaughter, and enough time must be allowed for the loss of blood that leads to the irreversible loss of brain function (Fuseini et al., 2017). Also, the Quran expressly forbids the consumption of blood among the Muslim community. In this regard, Kirton et al. (1981) indicated that poor bleeding-out at exsanguination often leads to poor keeping and eating quality. However, it must be noted that blood loss at exsanguination may not literally be completed because residual blood may still remain within the capillaries whether the animal is slaughtered with or without stunning. Therefore, religious ban on the consumption of blood must be interpreted as an intention for a proper bleeding, that is, “removing of blood as it is practically possible from the animal” (Fuseini et al., 2017, p. 128).
The Halal meat demand has been an increasing trajectory over the recent past (Farouk, 2013). Numerous factors that lead to the significant growth in the demand for Halal meat have been documented. For instance, Lever and Miele (2012) cited France and UK countries where for more than a decade, there has been exponential growth in the demand for meat that is slaughtered in accordance with the Halal rules. The current global expansion of Muslim communities may be the justification for the continued growth in the Halal meat market (Bergeaud-Blackler, 2004). Also, the increase in the export in Halal certified meat products from other countries such as the UK to the Muslim majority countries such as Indonesia, turkey, UAE, Malaysia, and Singapore has led to the growth of the Halal market globally (Fuseini et al., 2017).