Spectroscopy Training

Due: April 7

Weighting: 0%

All students are required to undertake the Kahn Academy course on spectroscopy before week 7

1. Please start this task in week 1 and make a plan to complete all modules by the end of week 6.

https://www.khanacademy.org/science/organic-chemistry/spectro scopy-jay.

Provisional Patent Application

Due: Week 1, Week 7, Week 14

Weighting: 25%

The practical work (synthesis and antibacterial structure activity relationship of sulfonamides) will be conducted in groups, with ~6 people per group.

1. You will prepare a group report in the style of a PATENT application by midday Week 14, Tuesday June 10 (5% group mark and 5% individual mark). This will also require submission of every group member's labbook as well as the FINAL patent applicaiton.
2. By the end of Week 1, each group will develop a written justification of their choice of final target compounds (2 compounds per student) and possible synthetic procedures (this contributes to your participation mark under point 3).
3. By the end of week 7, individual laboratory notebooks (hardcopy) will be submitted for marking AND each group will submit a formal write up of the experimental procedure ("Examples" section of the patent) for the synthesis of ONE of your sulfonamide final products for EACH student, including spectral data, written out in a chemistry Journal format. So if you have 6 group member, 6 examples are required (5% individual mark, no group mark). The Examples sections needs to be provided as one group document though marks will be allocated to individuals for their contribution. In addition, each group will submit the "Technical Field", "Background of the Invention" and "Object of the Invention" sections as hard-copy (not through turn-it-in) of their group's patent, written in patent format (5% group mark).

4. By midday week 14, Tuesday June 11, individual laboratory notebooks will be submitted for marking (5% individual mark). General safety and participation in the laboratory will also be considered in the mark. ,

Full details on what is expected for assessment of the practical component is provided in the laboratory manual and on the web site (see under “Laboratory Notes”).

Mid-semester test

Due: April 28

Weighting: 15%

There will be a 50 minute test (/15%) in Week 8, Tuesday May 28, 8 AM in the lecture session. This will cover up to the end of prodrugs. This is designed to give you specific feedback on your understanding of the topics up to this stage to assist you in your further study of the unit.

Quizzes

Due: in lectures and online

Weighting: 5%

Short quizzes (/5%) may be conducted at any time. Quizzes will also be conducted online. They are to allow identification of any deficiency in knowledge and understanding and to encourage continuous learning of the lecture material without the stress of a significant assessment component. Quizzes may contain questions from the spectroscopy workshop.

Pharmaceutical Agent Presentation

Due: May 12

Weighting: 5%

You will present a short oral on a clinically used pharmaceutical agent, providing information on its structure and function at a molecular level. Peer feedback will be provided. This will be conducted in the week 10 May 12 lecture/tutorial class session (8-10 AM). This will help in your consolidation of the medicinal chemistry concepts taught. The format is 3 minutes and 3 powerpoint slides including references.

Final exam

Due: week 15 (to be confirmed)

Weighting: 50%

The final exam (/50%) will be 3 hours in length with 10 minutes reading time. It is designed to assess specific understanding and holistic concepts of all the topics presented within the course and an opportunity for you to show what knowledge you have obtained and how you can apply this in new situations to solve complex problems.

Unit Web Page

The web page for this unit can be found at ilearn.mq.edu.au.

Just login and follow the prompts to CHEM3801/6801 Medicinal Chemistry.

You can use any web browser such as Firefox, Internet Explorer or Safari to login.

iLearn is the name for Macquarie University’s Learning Management System (LMS). The iLearn online learning environment enables learning, teaching, communication and collaboration. It is used to make lecture notes, laboratory notes, discussion forums, digital lecture recordings and other learning resources available to students online.

General

CHEM3801 is a 10 credit point unit and will require an average of 10 hours of work (contact and self study time) per week over the 15 weeks. For students with weak chemistry backgrounds, more time per week will probably be necessary to perform satisfactorily in this unit. CHEM3801 is run with three hours of lectures/tutorials per week, along with 4 hour blocks of laboratories/workshops. Students are expected to attend all lectures, tutorials and laboratory classes. Active participation by the students in all of these fora is encouraged.

• Lectures will be presented as a combination of formal lectures and interactive tutorial sessions. Some lecture material will be available on the unit web site, while other material will be provided in the lecture class. Learning is an active process, and as such, you must engage with the material. This means reading the textbook (and beyond) before and after lectures, attempting the assignment questions and other questions, discussing the concepts with your classmates and lecturers. Do not be afraid to ask questions – everyone benefits from a robust and open discussion of the topics.
• Quizzes and a mid session test will also be run in the lecture session. The in class quizzes will cover any material prior to that day’s lecture, therefore all students are expected to keep up to date with lecture material through revision each week. Online quizzes are also provided, with accompanying resources. The quizzes and mid session test are designed to allow you to continuously learn and to identify what you understand and the areas that you need to spend more time on, with minimal assessment penalty.
• All laboratory experiments will be conducted in groups. These have a highly collaborative and investigative approach, where you will be designing and synthesising a series of sulfonamides and subsequently testing them for antibacterial activity to determine the important features for their antibacterial activity. This laboratory work is designed to give real life experiences in research by involving students in the design of the experiments, using literature procedures as a guide, and trouble-shooting to identify the best experimental conditions. It will emphasise the importance of being well prepared, efficient and being fully aware of all safety procedures, proper recording and reporting of all data and interpreting of all results, and having an analytical and inquisitive approach. There will be 6 wet labs run in two streams (A and B) starting in Weeks 2/3.  There will be 7 dry labs.  The first one is in the 1000-level labs in week 1 (Friday 2-6PM) for the whole class where the semester’s lab work will be planned for your group.  Bring your laptop.  Another 6 dry labs to write up results and draft the patent will be held in the 2000/3000-level writeup room starting in weeks 3/2.

Further information on technology used: You are expected to access the unit web site frequently This contains important information including notes on the topics to be covered; the laboratory manual; What You Need to Know Sheets; your marks for practicals, quizzes and the mid-session exam; and past exam papers, including with answers. Additionally, the web site will also be used to post important messages and links to internet facilities and sites of relevance to the course, downloadable software, and lots of other interesting material.

All students are required to undertake the Kahn Academy course on spectroscopy before the end of the mid-semester break https://www.khanacademy.org/science/organic-chemistry/spectroscopy-jay. There are also resources in the library (PDF file in special reserve to help you with this.

If you do not have your own computer you may wish to access the Medicinal Chemistry web resources on campus using the PC computers in the Library or in the computer laboratories in 17 Wally's Walk. To view notes on all the topics and past exams on the unit web site, you will require Adobe Acrobat Reader Version 10 or later to be installed on your computer. Acrobat Reader can be downloaded from the Adobe web site https://get.adobe.com/reader/?loc=uk. If you are using the computers in the library, then Acrobat has already been installed. Please note information will also be sent by email to your student email account so please look at your email account on a frequent basis.

You are expected to access SciFinder Scholar and Reaxys to assist in searching the literature. These are available through the library web site.

Hand-held calculators will be occasionally used in tutorials and practicals, for tests and in the final examination. Note that text-retrieval calculators are not allowed in the in-semester tests or final examination.

Topics                                                           Lect/Tut         Lecturer

• Overview of Medicinal Chemistry                             wk 1-2             PK/JJ
  • Cellular targets of bioactive compounds
  • Binding of drugs to their targets
  • Agonists and antagonists  
• Protein structure and function                                     wk 2-3             JJ
  • Enzyme kinetics
  • Interaction of enzymes with inhibitors (competitive, non-competitive)
• Nucleic acids                                                              wk 4                JJ  
• Drug discovery from nature                                        wk 5-8             JJ
  • Drugs from synthesis
  • Optimisation of lead compound, structure-activity relationships
  • Physicochemical properties of drugs
  • Drug absorption, distribution, metabolism and excretion
  • Prodrugs
• Mid-semester test                                                       wk 8                JJ
• Quantitative structure-activity relationships              wk 9-10           PK
  • Case Study 1 (G-coupled protein receptor agonists and antagonists)
• 3 minute Pharmaceutical agent presentations             wk 10              PK/JJ
• Combinatorial Chemistry                                            wk 11              PK
  • Case Study 2 (Combinatorial discovery of non-peptide binding elements to Src SH3 domains)
  • Case Study 3 (antiviral prodrugs; the Case Study of Wuhan Coronavirus)
• Antibacterial agents                                                    wk 12-13         AP
  • Case Study 4 (betalactam antibiotics)
  • Case Study 5 (antifungals)

Wet labs are now on every second week with students doing labs in two streams, one doing wet labs in even weeks and the other doing wet labs in odd weeks. Students not doing wet labs will be workshoping their lab report/patent application.

mid-semester test has been moved to an earlier date (April 28, the first day back after Easter break)

new topic on antiviral prodrugs has been added

The in-lecture discussions of the lab reports has ben replaced with new lectures from AP