PHAR240 Drug Technologies and New Drug Therapies
Assignment 1 – Pre-Clinical Drug Development
Natural Product Screen for Novel Anti-Neoplastic Agents
Topic Selection Opens: Mon 4th July at 4:30pm
Topic Selection Closes: Sunday 10th July at 11:59pm
NOTE: choosing a topic is a mandatory component of this assessment
Submission Due Date: Wednesday 27th July by 11:59pm
NOTICE BEFORE WE BEGIN:
You are responsible for all information contained in this document and all associated documents for this assignment. You are strongly encouraged to print out copies of each document and to create a checklist for yourselves to ensure that you don’t miss anything.
This task provides you with training in data manipulation and analysis, graphical presentation of data, data interpretation, and use of scientific literature databases, as well as synthesis of the literature. These skills are not restricted to the pharmaceutical industry; many pharmacy practice research projects will require management of large datasets and running a small business can also require management of large amounts of data for government reporting. This assessment task focusses primarily on your ability to describe assays used in preclinical testing and applying their use to novel simulated drug-testing scenarios (ULO1), as well as assessing preclinical data in order to discuss their implications for drug development (ULO7). It is important to remember that we are training you for the plethora of professional pharmacist roles, not only for community pharmacy.
Regardless of the type of professional practice in which you will engage, by completing this assessment task, you will demonstrate your developing skills in the following areas:
- ability to assess preclinical data;
- apply your understanding of the assay involved in order to discuss the implications for drug development;
- evaluation of information and the sources of that information;
- synthesis of information into a coherent and logical piece of scientific writing;
- ability to communicate effectively, using language that is appropriate to the task, grammatically correct, well-structured and engaging;
- independence and time management; and
- ability to follow instructions.
PHAR240/Cytotoxicity Testing Assignment/2022/p.2
A Choice activity with the combinations of raw extracts and cancers is available in the Moodle site. A brief overview of the cancers and sources of the extracts is available at the end of this document. You are required to select ONE (1) combination for this assignment.
NOTE: selection of a combination is a mandatory component of this assignment
Each morning from Tuesday 5th July through Monday 11th July, data sets will be sent to those who made their selection the previous day. If you make a selection after data sets are released for the day, you will have to wait until the next day to receive your data. Once you receive your data set, you should start working on your assignment.
You are part of a well-funded research team comprised of chemists, pharmacologists, physiologists, and pharmacists at Sandstone University. Your group is interested in drug discovery with a focus on natural products. Recent discussions within your group have bolstered your interest in the discovery of novel anti-neoplastic drugs, and one of the pharmacologists in the group initiated the conversation with a reminder that several cancer drugs currently in use come from plants and marine products.
The chemists want to perform guided fractionation in collaboration with the pharmacologists to try to identify new lead compounds. Guided fractionation involves testing a raw extract (unpurified; in other words, put the material in a blender with some solvent and liquefy) on cultured cells to determine whether or not the extract possesses any cytotoxic activity. In subsequent experiments not addressed here, the chemist would subdivide the raw extract into additional extracts to be tested. It is very important to appreciate that a raw extract could contain hundreds of thousands of individual compounds. If one of these subdivided extracts demonstrates cytotoxic activity, further fractionation and testing rounds are continued until a purified compound has been obtained. Once those compounds have been isolated, the pharmacologists, physiologists and pharmacists will begin the pre-clinical testing.
A recording is available in the Lecture Recordings link that describes how to undertake the data analysis (PHAR240 Cytotox Data Analysis). Additionally, you will also find slides to accompany this recording, the assay protocol (Cytotoxicity Assay Protocol), a document to support the recording including aspects of the data manipulation and graphing (Experiment and Data Collection – please note that this is a shared document and therefore, your graph will only have 2 lines on it), the plate map to show which pieces of data correspond to which treatments (PHAR240 96-well Plate map), and some Excel Basics as a reminder. YouTube has videos to show you how to create a graph in Excel, in case you don’t remember from other units. PHAR240/Cytotoxicity Testing Assignment/2022/p.3
The overall format of your report is as follows. Please note that you are not required to provide a Methods section.
- Title Page: this must have the unit code and name, your name and student number, a title (choose your own), the due date, your word count and my name as the person responsible for this assignment. The format of this page is up to you.
- Introduction: you must provide sufficient background for the reader that they understand why this cancer is the focus of your investigation and why the extract is of potential value. With this in mind, you should address the following:
o provide a basic overview of the incidence of this cancer and who is most commonly affected (e.g. children, women, the elderly, etc.);
o provide an explanation, supported by the literature, to explain why this cancer requires new drugs; and
o provide a short commentary to address why the extracts chosen might represent a potential source of lead compounds for drug discovery.
§ NOTE: saying that a substantial number of people have this cancer does not explain why new drugs are needed; therefore, please think about this carefully
- Results: you must have at least one paragraph in your Results section, and it must appear before the graphs. Your purpose here is to draw the reader’s attention to the graphs that you have created (discussed as figures not graphs); in other words what does each graph show; what is noteworthy about each graph; and/or what aspects should draw the reader’s attention? In this section you can also compare data between graphs but this is not the place for the meaning of that comparison. It is important to remember that the meaning of the results is not mentioned here because the Results section is simply a description of the findings – the implications and meaning of the observations belongs in the Discussion section.
o PLEASE NOTE: from your data you might have 1 extract to pursue, more than 1 or none. It will depend entirely on the data with which you are supplied.
- Discussion: this is the section in which you will discuss the findings and identify which, if any, extracts have the potential to be pursued for guided fractionation. You must refer back to your graphs to explain why this/these is/are the extract(s) of interest. You are asked to use AT LEAST THREE (3) journal articles from the peer-reviewed literature to support your discussion of the results regarding which extract(s) to pursue.
o PLEASE NOTE: sites such as Up-to-Date do not count as a primary reference therefore, you should limit your use of such sites, or ideally, avoid them completely
- Conclusion: you will sum up your report, referring back to your comments in the Introduction regarding the need for new drugs for this particular cancer and the source of the extracts. You will then conclude the report.
- Reference List: you will use the APA format as outlined by the Academic Skills Office. The document is available in the PHAR240/440 Moodle site. Please note that as indicated in that document, in the sciences we do not use page numbers with the in-text reference. A total of FIVE (5) referencing errors (in-text or Reference list) will be permitted. Failure to use correct referencing format beyond this allowance will result in a 10% penalty.
- Analysis Table: due to problems in the past when some very unusual graphs were produced, you are required to supply ONE (1) example of your analysis tables. This
PHAR240/Cytotoxicity Testing Assignment/2022/p.4
would be the analysis of ONE (1) plate of data from ONE (1) cell line. This must appear
in the Appendix. Please note that this table needs to be large enough to be easily read.
For the report, please use a font equivalent to Arial 12pt. As you can see from the examples below, not all fonts are the same and so please choose your font wisely.
Arial 12pt Calibri 14pt
Times 14pt Cambria 14pt
The following style features are also mandatory:
- check to make sure that your document is formatted for A4 not US Letter (NOTE: US Letter is the default format for the Word program);
- entire document must be double-spaced;
- margins = 1.5cm top/bottom/right/left;
- header = 1.2cm header; footer = 1.2cm;
- you must have a running header at the top that has your surname and the unit code (if you do not know what a running header is, the running header for these instructions provides an example); and
- you must have pagination; however, it is up to you whether this appears in the header or the footer.
I have posted a Guide to Scientific Writing to help you with your report – please have a look at it before you proceed. It is very important that you do not misuse words such as “significant”, “prove/proved/proven” or “believe”. Do not use the first person (i.e. “I”) because in science we are obliged to be objective and report on the data as it stands, not our beliefs about it. I appreciate that in some fields there is a move away from objectivity but this is not acceptable for this report. Please be aware that you are not permitted to use direct quotes from any of your source articles.
DO NOT USE REPORTAGE. Your role is to synthesise information and use your critical thinking to paint a picture of the issue(s) under discussion, using the scientific literature to support your conclusions. Use of reportage makes it seem as if you are incapable of critical thinking; you are simply the mouthpiece of the opinions of others.
The following is an example of reportage (not acceptable):
According to Bozo and Boffo (2001) the sky is generally blue. This contrasts with the findings of Biffo et al. (1993), who found that the sky could appear grey, depending on the weather. A study by Whatshisname (2010) established that the sky could also have red or orange elements, depending on the atmospheric conditions.
The following is how you should be writing (acceptable approach):
While generally the sky is a shade of blue (Bozo and Boffo, 2001), it can vary from light blue to a blue that is almost black. However, depending on the climatic conditions, the
sky can appear grey (Biffo et al., 1993). Red or orange elements are quite common (Whatsisname, 2010), particularly at sunrise and sunset, depending on the atmospheric conditions. PHAR240/Cytotoxicity Testing Assignment/2022/p.5
This report has a word count of 1000 words, with an absolute maximum length of 1100 words, though I expect it to require less than that. Figure titles, figure legends, the initial table of extracts and cancer, any other table(s), and references do not count in the word count
Please note: this word count is not a “magic” number so you shouldn’t be trying to hit it exactly. That said do not exceed the stipulated absolute maximum word count.
CHOICE OF CULTURED CELL LINES:
Your team collaborates with a group at the National Cancer Institute (NCI) in Bethesda MD USA and they have generously donated cell lines for your research. As outlined above, you will choose ONE (1) cancer upon which to test your raw extracts, as represented by the cultured cell lines used as a model system. These cell lines are:
Set 1 = testicular cancer
F9 (mouse carcinoma)
NTERA-2 (human carcinoma)
Set 2 = lung cancer
H69AR (human carcinoma) KLN 205 (mouse carcinoma)
The cultured cell lines are derived from these types of cancer and are used as a model system for these types of cancer. You are not discussing the cell lines in any way: it is the cancer that is relevant, not the model system.
CHOICE OF MARINE EXTRACTS:
As part of this assessment, the combination that you choose will include TWO (2) extracts from the following list. Information about the source of these extracts and the person from whom you received them is outlined below. (All images courtesy of Prof Bruce Bowden, Chemistry Discipline, James Cook University)
Extract A represents an extract from a sea anemone shown in the image to the right. The extract is relatively insoluble in water and therefore, has been diluted in 10% ethanol (EtOH). This sample was collected off the coast of Orpheus Island by A/Prof Bozo Buffopolous, your collaborator at JCU in the Dept Chemistry.
PHAR240/Cytotoxicity Testing Assignment/2022/p.6
|Extract B is from the Bonaire flower coral and is seen in the image at the right. The sample was diluted in physiological saline after extraction. It was collected in Arcadia Bay at Magnetic Island by your collaborator Dr Lotsa Crasines. Dr Crasines is a member of the Dept Microbiology and Immunology at JCU.|
|Extract C is from the elegant moon/button polyps shown in the image to the right. It was diluted in deionised, distilled water (ddH2O). It was collected by A/Prof Buffopolous on the same dive trip on which he obtained the sample of sea anemone.|
|Extract D is from a stony cup coral shown in the image to the right. It is poorly soluble in water and only slightly soluble in ethanol and so it was dissolved in 10% EtOH. It was collected by your collaborator, Professor Whackum Goodus, of the Australian Institute of Marine Science (AIMS) on a dive trip to Fiji.|