Outline

Overview

This unit will explore the early phases of the drug discovery process from identification of a biological target molecule (enzyme or receptor) to identification of lead molecules and how chemical synthesis and biological screening is applied to develop lead molecules into drugs with desired molecular properties. Topics include drug discovery, protein structure and function, protein structure determination, drug synthesis, spectroscopic analysis, functional groups, molecular properties, molecular modelling, structure based drug design, drug screening. Students will also gain experience in a variety of experimental techniques related to drug design. In addition, students will develop skills including critical thinking, the use of information technology and report writing.

Unit details and rules

Unit code	PHAR5713
Academic unit	Pharmacy
Credit points	6
Prohibitions ?	None
Prerequisites ?	None
Corequisites ?	None
Assumed knowledge ?	6 credit points of Biochemistry, 12 credit points of Chemistry, 12 credit points of Pharmacology, 12 credit points of Physiology.
Available to study abroad and exchange students	No

Teaching staff

Coordinator	Thomas Balle, thomas.balle@sydney.edu.au
Lecturer(s)	David Hibbs, david.hibbs@sydney.edu.au
	Rebecca Roubin, rebecca.roubin@sydney.edu.au
	Jane Hanrahan, jane.hanrahan@sydney.edu.au
	Vivian Liao, vivian.liao@sydney.edu.au
Tutor(s)	Nathan Absalom, nathan.absalom@sydney.edu.au

Type	Description	Weight	Due	Length
Final exam (Record+)	Final exam Written Exam	60%	Formal exam period	2 hours
Outcomes assessed:
Assignment	Structure Based Drug Design Report Structure Based Drug Design Report	20%	Please select a valid week from the list below	2000 words + Figures
Outcomes assessed:
Online task	Online training modules MCQ	0%	Week 06	30 mins/30 questions
Outcomes assessed:
Assignment	Drug synthesis report and presentation Drug synthesis report and presentation	20%	Week 12	10 pages, 15 minutes
Outcomes assessed:
= hurdle task ? = group assignment ? = Type B final exam ?

Assessment summary

Online training modules: This is an online quiz. The quiz may be attempted as many times as necessary, however a mark of 25/30 must be obtained.
SBDD Report: Students write a report that covers the work performed in SBDD workshops 1-3. Students will work through a introductory toolbox exercise to acquire knowledge of three dimensional protein structures, drug receptor interactions, protein flexibility and basic molecular modelling tasks. Following on from that, students will create and validate a homology model of a nicotinic acetylcholine receptor. Validation will be based on assessment of protein backbone geometries and successful performance in ligand docking. In workshops 2 and 3 students will identify lead compounds using high throughput virtual screening and subsequently perform ligand optimisation to suggest a drug with improved docking score and physicochemical properties. Students following the online stream will collaborate with students on campus and participate in all aspects of the groupwork and report writing.
Drug synthesis report and presentation: Students will be required to design and synthesise a tripeptide compound. This lead compound will be characterised by analytical methods and it’s activity as an inhibitor of the enzyme chymotrypsin will be determined. Students will are expected to undertake library research on chymotrypsin inhibitors and peptide synthesis. Students will work in groups and data will be combined allowing a structure activity profile to be determined. Results will be presented orally and as formal report.
Drug synthesis report and presentation Online version: Students enrolled in the online stream will be allocated to an on-campus group and must follow labs remotely and participate in all group work, report writing and presentation. Upon return to campus an intensive lab skills session may be offered
Final exam: The final exam consists of both multiple-choice and short-answer questions, and will be based on lecture, lab and tutorial material.
You must obtain a minimum of 50% in the Final Exam AND a minimum of 50% across labs and workshops to pass this unit of study.
Group Work- Peer assessment (relative performance factor) will be applied to moderate the groupwork marks. Students will take part in a formative peer assessment conducted in early semester, and a summative peer assessment in late semester. Peer assessment will be completed online to obtain a factor between 0-1 and will be according to an agreed set of criteria established by groups in session 1
Repeating students: Exemption from components (laboratory, practical, forensics etc) for students repeating PHAR5713 will only be granted by the Year co-ordinator/ MPharm Program Director for students who achieved a grade of Credit (65%) or above for the relevant components in their previous attempt completed no more than three calendar years prior, and the relevant component has not significantly changed since the student completed it. Applications for exemption must be made in writing (which includes email) to the unit of study co-ordinator. Students who have been granted a component exemption in writing, together with any consequent change in the weighting of the remaining components in the unit of study, cannot attend the classes for that component and will have their overall mark for PHAR5713 based upon their performance in the remaining components in the unit of study. Component marks from a previous attempt will not be carried over. The exemption will not become effective until the student has accepted.

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	At HD level, a student demonstrates an aptitude for the subject and a well-developed understanding of the unit material. A ‘High Distinction’ reflects exceptional achievement and is awarded to students who demonstrate the ability to apply their subject knowledge and understanding to produce original solutions for novel or highly complex problems and/or comprehensive critical discussions of theoretical concepts.
Distinction	75 - 84	At DI level, a student demonstrates an aptitude for the subject and a well-developed understanding of the units material. A ‘Distinction’ reflects excellent achievement and is awarded to a student who demonstrates an ability to apply their subject knowledge and understanding of the subject to produce good solutions for challenging problems and/or a reasonably well-developed critical analysis of theoretical concepts.
Credit	65 - 74	At CR level, a student demonstrates a good command and knowledge of the unit material. A ‘Credit’ reflects solid achievement and is awarded to a student who has a broad general understanding of the units material and can solve routine problems and/ or identify and superficially discuss theoretical concepts.
Pass	50 - 64	At PS level, a student demonstrates proficiency in the material. A ‘Pass’ reflects satisfactory adequately referencing the original source of the work.
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

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:

Group Work - Non submission of peer assessment will result in a factor of zero (0) being applied to the non-submitter’s groupwork mark.

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.

Learning support

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.

Weekly schedule

WK	Topic	Learning activity
Multiple weeks	Lectures online	Lecture (19 hr)
	Structure determination, enzyme kinetics	Tutorial (8 hr)
	Structure based drug design	Computer laboratory (12 hr)
	Laboratory	Practical (12 hr)

Attendance and class requirements

Attendance: Students are expected to attend a minimum of 85% (10 out of 11 labs/workshops/tutorials) of compulsory activities for a unit of study, unless granted exemption by the Head of School or coordinator. The Head of School or coordinator most concerned may determine that a student fails a unit of study because of inadequate attendance. Alternatively, at their discretion, they may set additional assessment items where attendance is lower than 90%.

Same attendance requirements apply to students following the online stream.

Compulsory activities are all labs, workshops, tutorials, presentations and SBDD computer labs.

For more information see: https://www.sydney.edu.au/handbooks/medicine_health_PG/coursework_mr/pharmacy.shtml

If a tutorial/ lab/workshop is missed due to illness or misadventure, students are to submit a special consideration application along with supporting documentation. Students arriving more than 10 minutes after the commencement of the tutorial/ lab/ workshop will be marked as absent. Students swapping a class without prior approval from the UoS co-ordinator will be marked as 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.

G.L.Patrick (2013) An Introduction to Medicinal Chemistry, 5th Ed.

Learning outcomes

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.

Outcomes
Graduate qualities

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

LO1. demonstrate a working understanding of fundamental concepts and techniques of chemistry necessary for understanding drug analysis, delivery, drug action and therapeutics, and diagnostics
LO2. demonstrate an understanding of the mechanisms of action and the properties drugs display as biologically active molecules in living systems
LO3. identify sources of drugs, the way they are discovered, purified, characterised and analysed, and their physico-chemical properties
LO4. apply appropriate numeracy skills to the solution of pharmacy problems
LO5. engage in continuous reflection and take responsibility for personal and professional development
LO6. demonstrate appropriate attitudes and values in personal and professional dealings and business practice
LO7. demonstrate the ability to learn independently and take responsibility for your learning
LO8. demonstrate skills in time management, goal and priority setting, and self-evaluation
LO9. demonstrate a working understanding of fundamental concepts and techniques of pharmacology necessary for understanding drug action and analysis

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
Learning outcomes

Responding to student feedback

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

We have responded to student feedback to implement improvements in this unit.

Additional information

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.

Current students

Overview

Overview

Unit details and rules

Teaching staff

Assessment

Assessment

Assessment summary

Assessment criteria

Late submission

Academic integrity

Learning support

Learning support

Simple extensions

Special consideration

Using AI responsibly

Weekly schedule

Weekly schedule

Attendance and class requirements

Study commitment

Required readings

Learning outcomes

Learning outcomes

Graduate qualities

Outcome map

Responding to student feedback

Responding to student feedback

Additional information

Additional information

Disclaimer

On this page

Useful links

Media

Student links

About us

Connect

Current students

PHAR5713: Medicinal and Pharmaceutical Chemistry

Semester 1, 2021 [Normal day] - Camperdown/Darlington, Sydney

Overview

Overview

Unit details and rules

Teaching staff

Assessment

Assessment

Assessment summary

Assessment criteria

Late submission

Academic integrity

Learning support

Learning support

Simple extensions

Special consideration

Using AI responsibly

Weekly schedule

Weekly schedule

Attendance and class requirements

Study commitment

Required readings

Learning outcomes

Learning outcomes

Graduate qualities

Outcome map

Responding to student feedback

Responding to student feedback

Additional information

Additional information

Disclaimer

On this page

Useful links

Media

Student links

About us

Connect