- Title
- Generation of a virtual library of terpenes using graph theory, and its application in exploration of the mechanisms of terpene biosynthesis
- Creator
- Dendera, Washington
- Subject
- Terpenes
- Subject
- Plants -- Metabolism
- Subject
- Computational biology
- Subject
- Bioinformatics
- Subject
- Organic compounds -- Synthesis
- Subject
- Monoterpenes
- Subject
- Molecular biology -- Computer simulation
- Date Issued
- 2020
- Date
- 2020
- Type
- text
- Type
- Thesis
- Type
- Masters
- Type
- MSc
- Identifier
- http://hdl.handle.net/10962/123453
- Identifier
- vital:35439
- Description
- Terpenes form a large group of organic compounds which have proven to be of use to many living organisms being used by plants for metabolism (Pichersky and Gershenzon, 1934; McGarvey and Croteau, 1995; Gershenzon and Dudareva, 2007), defence or as a means to attract pollinators and also used by humans in medical, pharmaceutical and food industry (Bicas, Dionísio and Pastore, 2009; Marmulla and Harder, 2014; Kandi et al., 2015). Following on literature methods to generate chemical libraries using graph theoretic techniques, complete libraries of all possible terpene isomers have been constructed with the goal of construction of derivative libraries of possible carbocation intermediates which are important in the elucidation of mechanisms in the biosynthesis of terpenes. Virtual library generation of monoterpenes was first achieved by generating graphs of order 7, 8, 9 and 10 using the Nauty and Traces suite. These were screened and processed with a set of collated Python scripts written to recognize the graphs in text format and translate them to molecules, minimizing through Tinker whilst discarding graphs that violate chemistry laws. As a result of the computational time required only order 7 and order 10 graphs were processed. Out of the 873 graphs generated from order seven, 353 were converted to molecules and from the 11,7 million produced from order 10 half were processed resulting in the production of 442928 compounds (repeats included). For screening, 55 366 compounds were docked in the active site of limonene synthase; of these 2355 ligands had a good Vina docking score with a binding energy of between -7.0 and -7.4 kcal.mol-1. When these best docked molecules were overlaid in the active site a map of possible ligand positions within the active site of limonene synthase was traced out.
- Format
- 104 pages
- Format
- Publisher
- Rhodes University
- Publisher
- Faculty of Science, Microbiology and Biotechnology
- Language
- English
- Rights
- Dendera, Washington
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RU Department of Biochemistry and Microbiology (2015-)
| Thumbnail | File | Description | Size | Format | |||
|---|---|---|---|---|---|---|---|
| View Details Download | SOURCE1 | DENDERA-MSc-TR20-74.pdf | 2 MB | Adobe Acrobat PDF | View Details Download |