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Unit of study_

PCOL3012: Drug Design and Development

Semester 1, 2023 [Normal day] - Remote

Do you want to be the designer of the next billion dollar drug? In this unit of study you will apply your foundational knowledge and skills in medicinal chemistry and pharmacology to understand the discovery, design and development of major drug classes. You will gain knowledge into what makes a good drug target and how to design a new drug from lead drug identification to target optimisation. Drugs targeting a wide variety of genes, proteins, enzymes and receptors are explored through practicals and tutorials on molecular modelling and structure-activity relationships. The course also extends to a section on the design of diverse pharmacological agents, including compounds for imaging by positron emission tomography (PET) and drug applications based on proteomic and genomic big data. This unit of study is highly recommended for students interested in careers in drug discovery and development including pharmaceutical industry, government, and medical research pathways.

Unit details and rules

Unit code PCOL3012
Academic unit Pharmacy
Credit points 6
Prohibitions
? 
PCOL3912
Prerequisites
? 
(PCOL2011 or PCOL2021 or MEDS2002) or [BMED2401 and 6cp from (BMED2402 or BMED2405)] or 12cp from BCMB2XXX
Corequisites
? 
None
Available to study abroad and exchange students

Yes

Teaching staff

Coordinator Nial Wheate, nial.wheate@sydney.edu.au
Lecturer(s) Pegah Varamini, pegah.varamini@sydney.edu.au
Type Description Weight Due Length
Supervised exam
? 
Final examination
Examination including written questions - Pen and Paper type exam on campus
50% Formal exam period 2 hours
Outcomes assessed: LO1 LO2 LO3 LO4 LO5 LO6 LO7
Online task Online quiz
Multiple choice questions
5% Progressive 10 MCQs / 15mins
Outcomes assessed: LO1 LO5 LO4 LO3 LO2
Tutorial quiz Lecture and tutorial quiz
Multiple choice - In person
15% Week 08
Due date: 19 Apr 2023 at 12:00
60 minutes during lecture slot
Outcomes assessed: LO1 LO2 LO3 LO4 LO5 LO6 LO7
Presentation Individual drug: oral
Oral presentation
12.5% Week 09 5 minutes + 2 minutes questions
Outcomes assessed: LO1 LO2 LO3 LO4 LO5 LO6 LO7 LO8 LO9
Participation Individual drug: worksheet
One-page based on template - Must be completed in class
2.5% Week 09 One-page based on template
Outcomes assessed: LO1 LO2 LO3 LO4 LO5 LO6 LO7 LO8
Assignment group assignment Discipline project report
Written assessment with contribution assessed.
15% Week 10
Due date: 05 May 2023 at 23:59
8–10 pages, 1.5 spacing & 2cm margins
Outcomes assessed: LO1 LO2 LO3 LO5 LO6 LO7 LO8 LO9
group assignment = group assignment ?

Assessment summary

Detailed information for each assessment can be found on Canvas.

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

Information is clearly planned, presented logically, & well integrated; sophisticated grasp of the principles & interpretation including the possibility of theorizing/hypothesizing (evidence of originality of thought); references beyond lab material, lectures, textbooks and learning topics

Distinction

75 - 84

As above but without evidence of originality of thought; well written/ coherent/logical aand flows well; i.e. sentences are linked together; contains most surface knowledge (basic facts from provided materials with some material coming from other literature sources; references must be relevant).

Credit

65 - 74

Contains most surface knowledge (basic facts from provided materials with some material coming from other literature sources); lacks linking between sentences and paragraphs; an attempt has been made to incorporate the minimum of two references beyond lectures or textbook.

Pass

50 - 64

Important facts have been mentioned relevant to the question, but gaps in knowledge;
material may be correct but not entirely relevant; poor written expression and style

Fail

0 - 49

When you don’t meet the learning outcomes of the unit to a satisfactory standard.

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

To successfully complete this unit of study you must demonstrate a threshold (pass) standard of attainment of the unit of study learning outcomes as measured by performance on the unit of study summative assessments. Students who do not reach a threshold standard of proficiency of the learning outcomes will receive a mark no greater than 49 FA.   In addition, to pass the unit of study, you must participate in all assessment tasks and the end of semester theory examination: failure to participate in any one or more of these will result in a grade of Absent Fail (AF) for the unit.

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 1. Overview of course; Chirality and thalidomide; 2. Binding to a target - shape and intermolecular forces Lecture (2 hr) LO1 LO2 LO3 LO4 LO5 LO6
Molecular modelling 1 Practical (3 hr) LO1 LO2 LO3 LO4 LO5 LO7 LO8
Week 02 1. Quantitative structure activity relationships 1; 2. Quantitative structure activity relationships 2 Lecture (2 hr) LO1 LO2 LO3 LO4 LO5
Introduction Practical (1 hr) LO8 LO9
Week 03 1. Structure of drug targets: proteins; 2. Receptors as drug targets Lecture (2 hr) LO1 LO2 LO3 LO4 LO5 LO6 LO7
Synthesis Practical (3 hr) LO1 LO2 LO3 LO4 LO5 LO6 LO7 LO8 LO9
Week 04 1. Protein structure determination; 2. Proteins as a drug target: antivirals Lecture (2 hr) LO1 LO2 LO3 LO4 LO5 LO6
Activity Practical (3 hr) LO1 LO2 LO3 LO4 LO5 LO6 LO7 LO8 LO9
Week 05 1. Quantitative structure activity relationships: Opioids 1; 2. Quantitative structure activity relationships: Opioids 2 Lecture (2 hr) LO1 LO2 LO3 LO4 LO5 LO6
Molecular modelling 2 Practical (3 hr) LO1 LO2 LO3 LO4 LO5 LO7 LO8 LO9
Week 06 1. Polynucleotides as drug targets: cisplatin; 2. Isolation from nature Lecture (2 hr) LO1 LO2 LO3 LO4 LO5 LO6 LO7
Principles Tutorial (2 hr) LO1 LO2 LO3 LO4 LO5 LO6 LO7
Week 07 Tutorial Quiz Lecture (1 hr) LO1 LO2 LO3 LO4 LO5 LO6 LO7
Week 08 Analysis Practical (3 hr) LO1 LO2 LO3 LO4 LO5 LO6 LO8 LO9
1. Chelation therapy; 2. Drug Discovery: Finding a Lead Lecture (2 hr) LO1 LO2 LO3 LO4 LO5 LO6
Week 09 Molecular modelling 3 Practical (3 hr) LO1 LO2 LO3 LO4 LO5 LO8 LO9
1. Drug design: optimizing target interactions; 2. Kinase Inhibitors Lecture (2 hr) LO1 LO2 LO3 LO4 LO5 LO6 LO7
Week 10 1. Protein therapeutics 1; 2. Protein therapeutics 2 Lecture (2 hr) LO1 LO4 LO5 LO6 LO7
Week 11 1. Parameters used to describe drug activity; 2. Prodrugs and drug transformations Lecture (2 hr) LO1 LO2 LO3 LO4 LO5 LO7
Drug development Tutorial (2 hr) LO1 LO2 LO3 LO4 LO5 LO6 LO7
Week 12 1. Combinatorial synthesis; 2. PET and SPECT agents 1 Lecture (2 hr) LO1 LO2 LO3 LO4 LO5 LO7
Methods Tutorial (2 hr) LO6 LO7 LO9
Week 13 1. PET and SPECT agents 2; 2. Genomics, proteomics, big data & drug development Lecture (2 hr) LO1 LO6 LO7 LO9

Attendance and class requirements

Attendance: Attendance at a minimum of 80% of all timetabled classes is compulsory for successful completion of the course. Attendance will be recorded. If you do not show sufficient cause for absence from any part of the course you may not be allowed to sit the final examination. Absences from scheduled practical, workshop or tutorial sessions must be supported by appropriate documentation (you must also see guidelines for special consideration/arrangements for important information relating to absence from scheduled classes). Late arrival at classes (>15 minutes) without a valid reason will be counted as being absent.

 

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.

  • Recommended textbook: G.L. Patrick: An Introduction to Medicinal Chemistry (5th edition, Oxford University Press, 2013)

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. identify classes of pharmacologically important macromolecules as drug targets
  • LO2. recognise the role that structure and molecular properties (e.g. pKa, log P, log D) play in intramolecular interactions and their importance in drug action and design
  • LO3. explain principles underpinning the design of new drug molecules
  • LO4. explain principles underpinning the design of new protein therapeutics
  • LO5. understand the concept of a pharmacophore in drug-receptor interactions
  • LO6. explain various pharmacological assays used in drug discovery and interpret the significance of obtained data (e.g. IC 50, K)
  • LO7. demonstrate a basic understanding of various techniques and research fields (e.g. combinatorial chemistry, protein crystallography, PET, SPECT) and how they relate to drug discovery process
  • LO8. demonstrate confidence in the use of computer programs for studying pharmacology and for writing pharmacology reports
  • LO9. use the most relevant pharmacology and medicinal chemistry databases to locate specific papers, and to find relevant resources related to topics as allocated.

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.

Close the loop feedback on your Unit of Study Survey feedback will be provided via Canvas announcement following the release of marks.

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.