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Unit of study_

MCHM3901: From Molecules to Therapeutics (Advanced)

Semester 1, 2020 [Normal day] - Camperdown/Darlington, Sydney

Major changes to the way we discover and develop new medicines have taken place in recent years. Sequencing of the human genome has revolutionised drug target identification and therapeutic design. Genomics approaches that combine molecular biology and intensive data analysis are key to the development of personalised and precision therapies. New methods in organic synthesis have accelerated how we explore chemical space, developments in nanotechnology are driving innovative drug delivery methods. In this unit you will explore how these new ideas and technologies transforming medicinal chemistry. You will learn and apply such techniques to the molecular-level understanding of diseases and the design of effective therapeutics. You will learn the procedures leading to drug registration and regulation. You will participate in enquiry-led practicals that reinforce the concepts of the unit and develop your skills in cutting-edge methods used in modern medicinal chemistry. By studying this unit you will build knowledge and skills that will enable you to play a role in creating therapeutics that will impact lives. You will learn and apply such techniques to the molecular-level understanding of diseases and the design of effective therapeutics. The advanced unit has the same overall concepts as the mainstream unit but the material is discussed in a manner that offers a greater level of challenge and academic rigour. Students enrolled in the advanced stream will participate in alternative components, which may vary from year to year.

Unit details and rules

Unit code MCHM3901
Academic unit Chemistry Academic Operations
Credit points 6
Prohibitions
? 
MCHM3001
Prerequisites
? 
A mark of 70 or above in each of [(PCOL2011 or PCOL2021 or MEDS2002) or (BMED2401 and BMED2402) or (BMED2401 and BMED2405) or in each unit of (12cp from BCMB2XXX)] AND a mark of 70 or above in [(CHEM2401 or CHEM2521 or CHEM2911 or CHEM2915 or CHEM2921 or CHEM2991)]
Corequisites
? 
None
Assumed knowledge
? 

None

Available to study abroad and exchange students

Yes

Teaching staff

Coordinator Margaret Sunde, margaret.sunde@sydney.edu.au
Type Description Weight Due Length
Final exam hurdle task Final exam
Short answer and MCQ
40% Formal exam period 2 hours
Outcomes assessed: LO1 LO2 LO3
Assignment hurdle task Project report*
Results, Analysis and Summary organised and presented in LabArchive.
20% Multiple weeks Results submitted in LabArchive.
Outcomes assessed: LO3 LO4 LO6 LO8
Online task hurdle task Test 1
Online quiz - open book
5% Week 05 See Canvas
Outcomes assessed: LO1 LO3
Presentation hurdle task Presentation
Recorded presentation submitted online
10% Week 06 3 minute duration.
Outcomes assessed: LO5 LO6
Assignment group assignment In silico Docking Assignment Figure and Legend
Preparation of a representative and explanatory figure and figure legend.
10% Week 09 1 page.
Outcomes assessed: LO2 LO4 LO6 LO7
Small test hurdle task Test 2
Written test
5% Week 10 To be added by the unit coordinator
Outcomes assessed: LO1 LO5
Presentation hurdle task group assignment Group slide presentation
Presentation slides
10% Week 11 10-slide template provided.
Outcomes assessed: LO5 LO6 LO7
hurdle task = hurdle task ?
group assignment = group assignment ?

Assessment summary

  • Test 1 and 2: All in-semester assessments are compulsory, and failure to submit any piece of assessment will result in a grade of ‘AF Absent Fail’ for the unit of study.
  • Presentation: This involves the presentation of a research finding regarding a widely used therapeutic such as antibiotics, in the style of a short talk to a non-scientific audience.
  • Group slide presentation: This involves preparation of a presentation slide deck, using the template provided, with material describing the process of evaluation and approval of a drug for prescription in Australia.
  • Project report: Written report and data from lab work, organized and submitted through LabArchive.
  • Final exam: No sample papers will be provided.

Detailed information for each assessment can be found on Canvas.

* Lab / practical sessions and due dates for related assessment tasks for off-campus students impacted by the travel ban will be finalised once the ban has been lifted. The revised dates will be made available on the unit's Canvas site

Assessment criteria

The University awards common result grades, set out in the Coursework Policy 2014 (Schedule 1).

As a general guide, a high distinction indicates work of an exceptional standard, a distinction a very high standard, a credit a good standard, and a pass an acceptable standard.

Result name

Mark range

Description

High distinction

85 - 100

Mastery of topics showing extensive integration and ability to transfer knowledge to novel contexts; treatment of tasks shows an advanced synthesis of ideas; demonstration of initiative, complex understanding and analysis; work is very well presented; all criteria addressed and learning outcomes achieved to an outstanding level

Distinction

75 - 84

Excellent achievement, consistent evidence of deep understanding and application of knowledge in medical science; treatment of tasks shows advanced understanding of topics; demonstration of initiative, complex understanding and analysis; work is well-presented; all criteria addressed and learning outcomes achieved to a superior level

Credit

65 - 74

Confident in explaining medical science processes, with evidence of solid understanding and achievement; occasional lapses indicative of unresolved issues; treatment of tasks shows a good understanding of topic; work is well-presented with a minimum of errors; all criteria addressed and learning outcomes achieved to a high level

Pass

50 - 64

Satisfactory level of engagement with and understanding of topic; some inconsistencies in understanding and knowledge of medical science; work is adequately presented, with some errors or omissions, most criteria addressed and learning outcomes achieved to an adequate level

Fail

0 - 49

Unsatisfactory achievement and engagement with the medical science discipline; inadequate understanding or fundamental misunderstanding of topics; most criteria and learning outcomes not clearly or adequately addressed or achieved; lack of effort/involvement in the unit

For more information see sydney.edu.au/students/guide-to-grades.

For more information see guide to grades.

Late submission

In accordance with University policy, these penalties apply when written work is submitted after 11:59pm on the due date:

  • Deduction of 5% of the maximum mark for each calendar day after the due date.
  • After ten calendar days late, a mark of zero will be awarded.

This unit has an exception to the standard University policy or supplementary information has been provided by the unit coordinator. This information is displayed below:

All assignments must be submitted by the due date and quizzes and exams attended when they are scheduled. Students are expected to manage their time and to prioritise tasks to meet deadlines. Assessment items submitted after the due date without an approved extension using a special consideration or special arrangement form or request will incur penalties. Failure to meet assessment deadlines will incur mark deductions of 5% of the maximum awardable mark available for every day past the due date (for electronic submissions, days late includes Saturdays, Sundays and public holidays). These deductions will continue for 10 calendar days, until the solutions for the assignment are released, or marked assignments are returned to other students. At that point the mark awarded will be zero. For example, on an assignment given a mark of 70/100, the penalty would be 5 marks if submitted up to 24 hours late, resulting in a final mark of 65/100. If the assignment is submitted 6 days late, the penalty would be 30 marks and the final mark would be 40/100. If the assignment is more than 10 days late, submitted after the solutions for the assignment are released, or marked assignments are returned to other students, the final mark will be 0/100.

Academic integrity

The Current Student website  provides information on academic integrity and the resources available to all students. The University expects students and staff to act ethically and honestly and will treat all allegations of academic integrity breaches seriously.  

We use similarity detection software to detect potential instances of plagiarism or other forms of academic integrity breach. If such matches indicate evidence of plagiarism or other forms of academic integrity breaches, your teacher is required to report your work for further investigation.

You may only use artificial intelligence and writing assistance tools in assessment tasks if you are permitted to by your unit coordinator, and if you do use them, you must also acknowledge this in your work, either in a footnote or an acknowledgement section.

Studiosity is permitted for postgraduate units unless otherwise indicated by the unit coordinator. The use of this service must be acknowledged in your submission.

Simple extensions

If you encounter a problem submitting your work on time, you may be able to apply for an extension of five calendar days through a simple extension.  The application process will be different depending on the type of assessment and extensions cannot be granted for some assessment types like exams.

Special consideration

If exceptional circumstances mean you can’t complete an assessment, you need consideration for a longer period of time, or if you have essential commitments which impact your performance in an assessment, you may be eligible for special consideration or special arrangements.

Special consideration applications will not be affected by a simple extension application.

Using AI responsibly

Co-created with students, AI in Education includes lots of helpful examples of how students use generative AI tools to support their learning. It explains how generative AI works, the different tools available and how to use them responsibly and productively.

WK Topic Learning activity Learning outcomes
Week 01 Unit Introduction: History and future of drug discovery; Omics-informed drug discovery Lecture (2 hr) LO1
Week 02 Introduction to Practical Stream and NMR-based fragment screening Practical (3 hr) LO1 LO4
Omics in target and lead identification and drug evaluation Lecture (2 hr) LO1 LO2
Week 03 Enzyme assay and sample preparation for NMR based fragment screening Practical (3 hr) LO4
Expanding the druggable proteome; Therapeutic modulation of gene expression Lecture (2 hr) LO1
Data analysis, identification of fragment hits and molecular visualisation Practical (3 hr) LO3 LO4
Week 04 New models for pre-clinical screening; organoids and organ-on-a-chip Lecture (2 hr) LO1
Communicating drug development stories to a lay audience Workshop (3 hr) LO5 LO6
Week 05 Synthesis of drug discovery lead compound #1 Practical (3 hr) LO3 LO4
Hit discovery: high-throughput methods Lecture (1 hr) LO1
Synthesis of drug discovery lead compound #2 Practical (3 hr) LO3 LO5
Week 06 Synthesis of drug discovery lead compound #3 Practical (3 hr) LO3 LO5
Macrocycle and in silico screening Lecture (2 hr) LO1
Synthesis of drug discovery lead compound #4 Practical (3 hr) LO4 LO5 LO8
Week 07 Enzyme activity assays and determination of lead compound IC50 Practical (3 hr) LO4 LO6 LO8
Hit-to-lead approaches for optimising target Interactions Lecture (2 hr) LO1
Week 08 Optimising access to the target: Absorption, Distribution, Metabolism and Excretion Lecture (2 hr) LO1
In silico docking 1 Workshop (3 hr) LO2 LO5 LO6
In silico docking 2 Workshop (3 hr) LO2 LO5 LO6
Week 09 Lead optimisation and late-stage functionalisation Lecture (2 hr) LO1
Week 10 Economic challenges in drug discovery Lecture (1 hr) LO1
Week 11 Formulation and effective drug delivery methods Lecture (1 hr) LO1
Evaluating the use of animals in research Workshop (3 hr) LO1 LO8
Week 12 Clinical trials for pharmaceuticals and devices Lecture (2 hr) LO1
Week 13 Toxicology and safety; Registration of therapuetics Lecture (2 hr) LO1

Attendance and class requirements

Due to the exceptional circumstances caused by the COVID-19 pandemic, attendance requirements for this unit of study have been amended. Where online tutorials/workshops/virtual laboratories have been scheduled, students should make every effort to attend and participate at the scheduled time. Penalties will not be applied if technical issues, etc. prevent attendance at a specific online class. In that case, students should discuss the problem with the coordinator, and attend another session, if available.

Study commitment

Typically, there is a minimum expectation of 1.5-2 hours of student effort per week per credit point for units of study offered over a full semester. For a 6 credit point unit, this equates to roughly 120-150 hours of student effort in total.

Required readings

All readings for this unit can be accessed through the Library eReserve, available on Canvas.

  • Patrick, GL, (2016) An Introduction to Medicinal Chemistry 6th ed. Oxford University Press.

Learning outcomes are what students know, understand and are able to do on completion of a unit of study. They are aligned with the University's graduate qualities and are assessed as part of the curriculum.

At the completion of this unit, you should be able to:

  • LO1. demonstrate an understanding of major developments in modern drug discovery, ranging from analysis of bioinformatics through combinatorial synthetic methods and fragment-based screening, to formulation, preclinical development, delivery and registration.
  • LO2. apply bioinformatics and in silico methods to drug target identification and drug optimisation
  • LO3. propose and justify reasonable synthetic approaches towards small organic molecule drug candidates
  • LO4. Understand and apply the principles of scientific measurement during a fragment-based screening project.
  • LO5. find and analyse information and judge its reliability and significance when evaluating the efficacy of drug action.
  • LO6. communicate scientific information appropriately, both orally and through written work
  • LO7. engage in team and group work to assess the development, approval and registration of new drugs
  • LO8. demonstrate a sense of responsibility, ethical behaviour, and independence as a learner and as a scientist.

Graduate qualities

The graduate qualities are the qualities and skills that all University of Sydney graduates must demonstrate on successful completion of an award course. As a future Sydney graduate, the set of qualities have been designed to equip you for the contemporary world.

GQ1 Depth of disciplinary expertise

Deep disciplinary expertise is the ability to integrate and rigorously apply knowledge, understanding and skills of a recognised discipline defined by scholarly activity, as well as familiarity with evolving practice of the discipline.

GQ2 Critical thinking and problem solving

Critical thinking and problem solving are the questioning of ideas, evidence and assumptions in order to propose and evaluate hypotheses or alternative arguments before formulating a conclusion or a solution to an identified problem.

GQ3 Oral and written communication

Effective communication, in both oral and written form, is the clear exchange of meaning in a manner that is appropriate to audience and context.

GQ4 Information and digital literacy

Information and digital literacy is the ability to locate, interpret, evaluate, manage, adapt, integrate, create and convey information using appropriate resources, tools and strategies.

GQ5 Inventiveness

Generating novel ideas and solutions.

GQ6 Cultural competence

Cultural Competence is the ability to actively, ethically, respectfully, and successfully engage across and between cultures. In the Australian context, this includes and celebrates Aboriginal and Torres Strait Islander cultures, knowledge systems, and a mature understanding of contemporary issues.

GQ7 Interdisciplinary effectiveness

Interdisciplinary effectiveness is the integration and synthesis of multiple viewpoints and practices, working effectively across disciplinary boundaries.

GQ8 Integrated professional, ethical, and personal identity

An integrated professional, ethical and personal identity is understanding the interaction between one’s personal and professional selves in an ethical context.

GQ9 Influence

Engaging others in a process, idea or vision.

Outcome map

Learning outcomes Graduate qualities
GQ1 GQ2 GQ3 GQ4 GQ5 GQ6 GQ7 GQ8 GQ9

This section outlines changes made to this unit following staff and student reviews.

This is the first time this unit has been offered.

Work, health and safety

We are governed by the Work Health and Safety Act 2011, Work Health and Safety Regulation 2011 and Codes of Practice. Penalties for non-compliance have increased. Everyone has a responsibility for health and safety at work. The University’s Work Health and Safety policy explains the responsibilities and expectations of workers and others, and the procedures for managing WHS risks associated with University activities.

General Laboratory Safety Rules

  • No eating or drinking is allowed in any laboratory under any circumstances 
  • A laboratory coat and closed-toe shoes are mandatory 
  • Follow safety instructions in your manual and posted in laboratories 
  • In case of fire, follow instructions posted outside the laboratory door 
  • First aid kits, eye wash and fire extinguishers are located in or immediately outside each laboratory 
  • As a precautionary measure, it is recommended that you have a current tetanus immunisation. This can be obtained from University Health Service: unihealth.usyd.edu.au/

Disclaimer

The University reserves the right to amend units of study or no longer offer certain units, including where there are low enrolment numbers.

To help you understand common terms that we use at the University, we offer an online glossary.