Nowadays, cancer treatment is not only a quest of eliminating cancer cells by induction of cell apoptosis. New curative strategies also include targeting the tumour micro-environment, preventing angiogenesis, regulating the immune response or the chronic inflammation that is commonly associated with cancer. And for the last few decades, we have known that plants provide a wide platform of potential drug substances for cancer therapy with all-around mechanisms, effects and targets.
- Colon Cancer
Figure 2.2 Diagram shows the differences between normal & cancerous colon
Colon cancer or colorectal cancer occurs in the lining of the colon and rectum. The colon and rectum are part of the digestive system which their main function is to remove waste from the body as well as to absorb nutrients and water. Colon cancer patients might have a higher rate of survival and recovery if the cancer with early detection but, unfortunately, colon cancer would not be showing any symptoms or sign until it reached the final stage (TerziÄ‡, & et al, 2010). Some of the major symptoms of colon cancer including rectal bleeding, frequent bowel movements, iron loss, mucous discharge from the anus, dark stools called melena, rheumatism, and hemorrhoids. The tumor wills eventually blocks the bowel as it is growing in the colon which will lead to further infection or bleeding in the abdominal cavity in the gut. In worst case scenario, the tumors will metastasized and start infecting other organs and cause another problems in the body, for example; loss of appetite, liver pains, and even cancer to another organs. (Labianca, & et al, 2010)
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Even though it is one of the best-understood neoplasms as from the genetic perspective, colon cancer is the second leading cause of cancer-related deaths. This is somehow shows that some of the cancer cells are not completely destroyed by current therapies. Therefore, what is need or has yet to be enacted is whether every colon cancer cell has the potential to start and continue tumor growth, or whether the tumor is hierarchically formed so that only a subgroup of cancer stem cells has such possibility.
1.2 Arabidopsis thaliana
Arabidopsis thaliana is a crucial model organism for plant biology, providing as a major source for studies of plant physiology, genetics, and molecular biology. Its use as a model species is expedited by its production of vast numbers of seeds, its fast generation time in the laboratory, and its reproduction generally by self-fertilization. Many of the similar traits that contribute to the uses of A. thaliana as a model organism are significant in finding the habitat of the species in its natural environment. (François, & et al, 2008)
There are few reasons why A. thaliana would be a very good candidate to extract the Lupeol for this research. Firstly, the A. thaliana plant is very small. Following germination, the plant seedling produces a series of leaves on a short stem, resulting in a compact rosette close to the soil. The small size allows large numbers of A. thaliana plants to be grown indoors in growth chambers and greenhouses, preventing the requirement for researchers to have access to field plots. (Haughn, & Kunst, 2010)
Secondly, relative to other seed plants, the generation time of A. thaliana is short. Under standard conditions of light and temperature, it will flower within a month and produce mature seeds within two months. The time from seed to seed can be shortened by two weeks if plants are grown under continuous light. (Haughn, & Kunst, 2010)
Lastly, the self-fertility and large numbers of progeny simplify the analyses of inheritance and the maintenance of genetic stocks. Also, the small diploid genome which is 125 mega base pairs has significantly reduces the amount of labour and time needed to clone and manipulate genes. (Haughn, & Kunst, 2010)
Figure 1.3 Arabidopsis thaliana plant
1.3 COMPUTATIONAL MOLECULAR ANALYSIS (IN-SILICO)
Due to advancing computational methods, drug design can now be performed by in-silico. The definition of in-silico from the journalist according to the methods that include homology models, quantitative structure-activity relationships, databases, pharmacophores and other molecular modelling approaches such as data mining, network analysis tools, data analysis tools, and machine learning that use a computer. In-silico processes are generally used together with bundles of in-vitro data both to create and to evaluate the model. In-silico studies are not meant to replace the traditional lab methods. Instead, they are meant to augment and reduce the amount of time spent on pilot study. In-silico studies were performed on computers which can make highly accurate calculations especially when it comes to mathematical models. An example of this with association to drug design is molecular docking. Tools that are commonly used for the in-silico molecular analysis process are divided into online tools and downloadable software. Among the software used online mainly from EMBL-EBI platform are ClustalOmega, ClustalW, MUSCLE, PDBsum, and many others. The example of downloadable software that is commonly used is PhyloDraw, ClustalX, ClustalW2, Swiss PDB Viewer, PyMOL, and Autodock Tools. (Goujo, et al., 2010)
1.4 CANCER COMPUTATIONAL BIOLOGY
Cancer computational biology is an area that is designed to determine the future of cancer mutations, through an algorithmic approach and data analysis. Research in this area has led to the use of high-throughput measurements. High-throughput measurements have enabling the collection of millions of data points using robotics and other sensors. These data were collected from DNA, RNA, and other biological structures. The areas of interest are including the determination of the tumor’s characteristic, an analysis to determine the molecular that causing cancer, and to understand how the human genome is associated with tumor development and cancer. (Yakhini, & Jurisica, 2011)
1.5 PROBLEM STATEMENT
Although there are vast amount of researches already done onto this plant, there are no specific researches on in-silico docking between Lupeol of Arabidopsis thaliana with mutant APC protein that causing colorectal cancer. This somehow has open an opportunity to investigate either this research may lead to a successful ligand binding or molecular interactions between ligand and corresponding receptor which in this case is the mutant APC protein. A molecular understanding of the events could lead to anticancer neutralization, enhancement or escape that will eventually be critical to the improvement of drugs against cancer cells.
1.6.1 General Objective
To propose that an anti-cancer properties of Lupeol present in the Arabidopsis thaliana can be used as an alternative mean to stop colon cancer in humans.
1.6.2 Specific Objectives
- To examine either the Lupeol that will be found in this study binds successfully to the APC protein responsible for the mutation.
- To investigate the capability of Lupeol to overcome this mutation without any lasting side effects or toxicity to the human body.
- To ascertain the induction of apoptosis by Lupeol into the cancer cells together with a comparison to the currents drugs.
1.7.1 Null Hypothesis
The Lupeol found in Arabidopsis thaliana cannot be used to stop colon cancer.
1.7.2 Alternate Hypothesis
The Lupeol found in Arabidopsis thaliana can be used to stop colon cancer.
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