Students
MOLS8851 – Advanced Medicinal Chemistry
2020 – Session 2, Weekday attendance, North Ryde
Notice
As part of Phase 3 of our return to campus plan, most units will now run tutorials, seminars and other small group learning activities on campus for the second half-year, while keeping an online version available for those students unable to return or those who choose to continue their studies online.
To check the availability of face to face activities for your unit, please go to timetable viewer. To check detailed information on unit assessments visit your unit's iLearn space or consult your unit convenor.
General Information
Download as PDF
| Unit convenor and teaching staff |
Unit convenor and teaching staff
Lecturer and co-convenor
Joanne Jamie
Contact via 98508283
4 Wally's Walk room 231
Have an open door policy, but students are encouraged to arrange a meeting via email.
Lecturer and Co-convenor
Peter Karuso
Contact via 9850 8290
4WW 232
Have an open door policy, but students are encouraged to arrange a meeting via email.
Lecturer and tutor
Vaughan Moon
Contact via 9850 8309
4 Wally's Walk room 204
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| Credit points |
Credit points
10
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| Prerequisites |
Prerequisites
Admission to GradDipBiotech or GradCertLabAQMgt or GradDipLabAQMgt or MBiotech or MBioBus or MLabAQMgt or MRadiopharmSc or MSc or MScInnovationChemBiomolecularSc and (CHEM6801 or CBMS606)
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| Corequisites |
Corequisites
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| Co-badged status |
Co-badged status
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| Unit description |
Unit description
This unit builds on the fundamentals of medicinal chemistry, including the discovery, design and development of new medicines. The aim of the unit is to integrate chemical biology and organic chemistry to reveal how these are used in medicinal chemistry to design and synthesise new drugs and to understand their mode of action. The unique aspect of this unit is the focus on computational chemistry in the field of drug design and development. This includes aspects of molecular modelling, molecular dynamics, docking, pharmacophore modelling and QSAR as they relate to the understanding of drug action and design of new drugs.
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Important Academic Dates
Information about important academic dates including deadlines for withdrawing from units are available at https://www.mq.edu.au/study/calendar-of-dates
Learning Outcomes
On successful completion of this unit, you will be able to:
- ULO1: Apply the principles of rational drug design for the creation of drug libraries.
- ULO2: Exploit structure activity relationships (SAR) and quantitative structure activity relationships (QSAR) principles to determine drug modes of action.
- ULO3: Design the structure of small molecules by combining the principles of drug design to create potential new drugs.
- ULO4: Communicate the above advanced medicinal chemistry concepts competently in oral presentations and in written format in the form of a report and a final exam.
- ULO5: Research and communicate a contemporary topic in medicinal chemistry through oral and online discussion.
General Assessment Information
The final exam is a 3 hr written exam.
Assignments are based on the previous 2 weeks work.
The report is a major work that you will start preparing in week 5 and complete in week 13. It involves a written report.
The oral presentation will be a 5 - 10 minute talk on a contemporary topic related to medicinal chemistry with an online discussion component.
The weekly classes are a participation hurdle and failure to participate in at least 10 of the 13 weekly classes will result in you failing CBMS842. Participation includes active engagement with the weekly tasks and in class objectives.
If you are unable to attend a class, please contact Peter Karuso (peter.karuso@mq.edu.au) or Joanne Jamie (joanne.jamie@mq.edu.au) immediately. In addition, you must submit a Special Consideration request at ask.mq.edu.au to justify your absence.
Your marks will be placed on the CBMS842 iLearn site.
Your final grade will be based on the mark from the aggregation of the individual assessments, with 50% or greater needed overall for a pass.
Medical certificates or other official documents must be lodged as part of a Special Consideration request at ask.mq.edu.au as soon as possible if you are absent for any of the weekly classes or miss the due date for any of the assessment tasks. If your reason is regarded as valid for missing an assignment you will be given an average of the other assignments. If you miss the final exam for a valid reason, a supplementary exam will be provided. Any assessment tasks not submitted on time that does not get approval through the Special Consideration request will get a 10% deduction of marks for every weekday late.
Final Examination Details: The examination timetable will be available in Draft form approximately eight weeks before the commencement of the examinations and in final form approximately four weeks before the commencement of the examinations. You are expected to present yourself for examination at the time and place designated by the University in the Examination Timetable. This could be any day after the final week of semester and up until the final day of the official examination period. It is Macquarie University policy to not set early examinations for individuals or groups of students. All students are expected to ensure that they are available until the final day of the official examination period.
The only exception to sitting an examination at the designated time is because of documented illness or unavoidable disruption. Absence from the final exam will result in a grade of F except in the case of a genuine medical emergency or misadventure as defined by the University (see below). In these circumstances you should apply for a Supplementary Exam at ask.mq.edu.au. NOTE: If you apply for a Supplementary Examination, you must make yourself available for the Supplementary Exam times in early December - specific examination dates and times will be determined at a later date. If you are not available at that time, there is no guarantee an additional examination time will be offered.
Assessment Tasks
| Name | Weighting | Hurdle | Due |
|---|---|---|---|
| Research Report | 20% | No | Week 13 |
| Oral Presentation | 10% | No | Weeks 4 & 12 |
| Final Exam | 50% | No | Eaxamination Period |
| Five Assignments | 15% | No | Weeks 4, 6, 8, 10 & 12 |
| Class participation | 5% | Yes | Weeks 1-13 |
Research Report
Assessment Type 1: Report
Indicative Time on Task 2: 18 hours
Due: Week 13
Weighting: 20%
Using what you have learnt, pick a drug target, research what is known about this target and summarise the relevant literature and design your own compounds to test. Present this review in a written report.
On successful completion you will be able to:
- Apply the principles of rational drug design for the creation of drug libraries.
- Exploit structure activity relationships (SAR) and quantitative structure activity relationships (QSAR) principles to determine drug modes of action.
- Design the structure of small molecules by combining the principles of drug design to create potential new drugs.
- Communicate the above advanced medicinal chemistry concepts competently in oral presentations and in written format in the form of a report and a final exam.
Oral Presentation
Assessment Type 1: Presentation
Indicative Time on Task 2: 12 hours
Due: Weeks 4 & 12
Weighting: 10%
An oral presentation and class discussion (including online) on a contemporary medicinal chemistry topic.
On successful completion you will be able to:
- Communicate the above advanced medicinal chemistry concepts competently in oral presentations and in written format in the form of a report and a final exam.
- Research and communicate a contemporary topic in medicinal chemistry through oral and online discussion.
Final Exam
Assessment Type 1: Examination
Indicative Time on Task 2: 30 hours
Due: Eaxamination Period
Weighting: 50%
This is a 3 hr final exam
On successful completion you will be able to:
- Apply the principles of rational drug design for the creation of drug libraries.
- Exploit structure activity relationships (SAR) and quantitative structure activity relationships (QSAR) principles to determine drug modes of action.
- Design the structure of small molecules by combining the principles of drug design to create potential new drugs.
- Communicate the above advanced medicinal chemistry concepts competently in oral presentations and in written format in the form of a report and a final exam.
Five Assignments
Assessment Type 1: Quiz/Test
Indicative Time on Task 2: 25 hours
Due: Weeks 4, 6, 8, 10 & 12
Weighting: 15%
5 assignments, each worth 3% - short assignments based on previous 2 weeks of classes.
On successful completion you will be able to:
- Apply the principles of rational drug design for the creation of drug libraries.
- Exploit structure activity relationships (SAR) and quantitative structure activity relationships (QSAR) principles to determine drug modes of action.
- Design the structure of small molecules by combining the principles of drug design to create potential new drugs.
Class participation
Assessment Type 1: Participatory task
Indicative Time on Task 2: 13 hours
Due: Weeks 1-13
Weighting: 5%
This is a hurdle assessment task (see assessment policy for more information on hurdle assessment tasks)
Participation in the weekly classes is a hurdle and you are expected to attend all classes. In the event of illness or misadventure, you can justify your absence from a class by submitting a Special Consideration request.
On successful completion you will be able to:
- Apply the principles of rational drug design for the creation of drug libraries.
- Exploit structure activity relationships (SAR) and quantitative structure activity relationships (QSAR) principles to determine drug modes of action.
- Design the structure of small molecules by combining the principles of drug design to create potential new drugs.
- Communicate the above advanced medicinal chemistry concepts competently in oral presentations and in written format in the form of a report and a final exam.
- Research and communicate a contemporary topic in medicinal chemistry through oral and online discussion.
1 If you need help with your assignment, please contact:
- the academic teaching staff in your unit for guidance in understanding or completing this type of assessment
- the Writing Centre for academic skills support.
2 Indicative time-on-task is an estimate of the time required for completion of the assessment task and is subject to individual variation
Delivery and Resources
This is a self taught unit using the "molecular conceptor" and MOE software. Each week a set number of tasks are assigned and assessed. There is no text book set for this unit but the material covered in CHEM6801/CBMS606 (Medicinal Chemistry) is assumed knowledge as is at least 2000-level Organic Chemistry
Unit Schedule
WEEK 1
- Introduction to Drug Discovery
- Principles of Rational Drug Design
WEEK 2
- Structure Activity Relationships (SAR)
- Bioisosterism
WEEK 3
- Bioinformatics
- Protein Structure
WEEK 4
- Library Design
- Molecular Graphics
WEEK 5
- Molecular Geometry
- Molecular Energies
- Conformational Analysis
WEEK 6
- Protein Ligand Binding
- Principles of Structure Based Design
WEEK 7
- Molecular Docking: Principles and Methods
WEEK 8
- Case Studies - Structure Based Design
- Case Studies - Docking in Drug Discovery
- Analysis of Protein Ligand Complexes
WEEK 9
- Principles in Pharmacophore elucidation
- Ligand based Approaches
WEEK 10
- Examples of Pharmacophores
- Case Studies - Ligand Design
WEEK 11
- QSAR: Principles and Methods
- Case Studies - QSAR and 3D-QSAR
WEEK 12
- Project Completion
WEEK 13
- Project submission
- Review
MOE WORKSHOPS
- Introduction to MOE
- Building Molecules
- 3D Visualisations
- Structure based design
- Docking
- Ligand based design
- Protein Ligand Interaction footprints
Policies and Procedures
Macquarie University policies and procedures are accessible from Policy Central (https://staff.mq.edu.au/work/strategy-planning-and-governance/university-policies-and-procedures/policy-central). Students should be aware of the following policies in particular with regard to Learning and Teaching:
- Academic Appeals Policy
- Academic Integrity Policy
- Academic Progression Policy
- Assessment Policy
- Fitness to Practice Procedure
- Grade Appeal Policy
- Complaint Management Procedure for Students and Members of the Public
- Special Consideration Policy (Note: The Special Consideration Policy is effective from 4 December 2017 and replaces the Disruption to Studies Policy.)
Students seeking more policy resources can visit the Student Policy Gateway (https://students.mq.edu.au/support/study/student-policy-gateway). It is your one-stop-shop for the key policies you need to know about throughout your undergraduate student journey.
If you would like to see all the policies relevant to Learning and Teaching visit Policy Central (https://staff.mq.edu.au/work/strategy-planning-and-governance/university-policies-and-procedures/policy-central).
Student Code of Conduct
Macquarie University students have a responsibility to be familiar with the Student Code of Conduct: https://students.mq.edu.au/study/getting-started/student-conduct
Results
Results published on platform other than eStudent, (eg. iLearn, Coursera etc.) or released directly by your Unit Convenor, are not confirmed as they are subject to final approval by the University. Once approved, final results will be sent to your student email address and will be made available in eStudent. For more information visit ask.mq.edu.au or if you are a Global MBA student contact globalmba.support@mq.edu.au
Student Support
Macquarie University provides a range of support services for students. For details, visit http://students.mq.edu.au/support/
Learning Skills
Learning Skills (mq.edu.au/learningskills) provides academic writing resources and study strategies to help you improve your marks and take control of your study.
The Library provides online and face to face support to help you find and use relevant information resources.
Student Services and Support
Students with a disability are encouraged to contact the Disability Service who can provide appropriate help with any issues that arise during their studies.
Student Enquiries
For all student enquiries, visit Student Connect at ask.mq.edu.au
If you are a Global MBA student contact globalmba.support@mq.edu.au
IT Help
For help with University computer systems and technology, visit http://www.mq.edu.au/about_us/offices_and_units/information_technology/help/.
When using the University's IT, you must adhere to the Acceptable Use of IT Resources Policy. The policy applies to all who connect to the MQ network including students.
Changes from Previous Offering
There have been minor changes to the order of topics and assessment structure. The classes have been set up such that on-campus attendance is not required but will run as normal for 4 h every week.