On line quizzes are multiple choice questions on the previous 2 weeks work.

The report and presentation is a major work that you will start preparing in week 5 and complete in week 13.  It involves a written report and a powerpoint presentation (15 minutes)

The final exam is a 3 hr written exam

Your marks (in-class and online quizzes, report and presentation) will be placed on the CBMS842 web 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 official documents must be lodged as part of a disruption to studies request at ask.mq.edu.au as soon as possible if you are absent for any of the assessment tasks or miss the due date for any of the on-line tasks.  If your reason is regarded as valid for missing the in-class quizzes, you will be given an average of the other quizzes done; with the on-line quizzes an extension of time will be provided if the disruption to studies request is approved.  If you miss the mid-session test or final exam for a valid reason, a supplementary test/exam will be provided.  An extension for submission of the lab reports/lab books will also be provided if the disruption to studies approval is obtained.  Any assessment tasks not submitted on time that does not get approval through the disruption to studies 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 end of the teaching semester, that is, 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 week of December 11 – 15, 2017.  If you are not available at that time, there is no guarantee an additional examination time will be offered. Specific examination dates and times will be determined at a later date.

This is a self taught unit using the "molecular conceptor" software.  Each week a set number of tasks are assigned and assessed. There is no text book set for this unit but the material in the CBMS306 text book (Patrick, "Medicinal Chemistry", 5th Ed) is assumed knowledge.

Week 1 introduction

                A1. INTRODUCTION TO DRUG DISCOVERY 

                A2. PRINCIPLES OF RATIONAL DRUG DESIGN 

                A2.3 Receptor-Based Design

                A2.4 Integration in a Global Perspective 

                A2.5 Challenge of the Genomics Era 

                A2.6 Typical Projects 

Week 2 Molecular basis of drugs

                J1. MOLECULAR GEOMETRY 

                J4. MOLECULAR ENERGIES 

                J6.3 Visualization 

                J6.4 Editing & Manipulation 

                J6.5 Surfaces & Volumes 

                J6.6 Visualizing Interactions 

Week 3 Library design

                C1 Introduction

                C2 Basis of a good scaffold

                C3 Scaffold selection and design

                C4 Focussed and diverse strategies

                C5 measuring distances

                C8 Increasing quality of the library

                C9 Example of library analysis

                C3. CASE STUDIES IN LIBRARY DESIGN 

                                C3.2.1 Case Study-Diaminopyrimidines DHFR inhibitors

                                C3.1 Case Study-1 : CDK2 Inhibitors 

Week 4 Protein structure function & MD

                E1. STRUCTURAL BIOINFORMATICS 

                E2. PROTEIN STRUCTURE 

                E3. MOLECULAR DYNAMICS 

Week 5 SAR

                A3.1 Introduction                  A3.2 Probing H-Bond Interactions 

                A3.3 Probing Ionic Interactions 

                A3.4 Probing Hydrophobic Interactions 

                A3.5 Probing Other Interactions 

                A3.6 Modifications to Alter the Geometry of the Ligand 

                A3.7 Complexity of SAR Analyses 

                A3.8 Example of Good Exploitation of SAR Complexity 

Week 6 SAR case studies

                A1.1 Case Study-1 : Banyu Example 

                A1.2 Case Study-2 : Dioxobenzothiazole Example 

                A1.3 Case Study-3 : EGF-R Kinase Inhibitors 

                A1.4 Case Study-4 : Nifedipine Example 

                A1.5 Case Study-5 : Carbonic Anhydrase Example 

                A1.6 Case Study-6 : β-Lactam Antibiotics 

                A1.7 Case Study-7 : Anilino-Quinazoline Example 

                B3.8 Case Study-8 : Salicylamide Mimics 

Week 7 Structure based design

                E1. INTRODUCTION TO PROTEIN-LIGAND BINDING 

                E1.2 Analytical Process 

                E1.3 Principles of Analysis 

                E1.4 Example of Tight Interactions 

                E1.5 Receptor & Ligand Flexibility 

                E1.6 Role of the Solvent 

                E1.7 Prediction of Binding Modes 

                E1.8 Methods for Analyzing Binding 

2. PRINCIPLES OF STRUCTURE-BASED DESIGN 

                 E2.1 Introduction 

                E2.3 The Four Design Methods 

                E2.4 Analog Design 

                E2.5 Database Searching 

                E2.7 Manual Design 

                E2.8 Another Iteration 

                E2.9 A Success Story 

                E2.10 Conclusion 

Week 8 Molecular docking

Week 9 case studies - structure based design & molecular docking

Week 10 Ligand based design

Week 11 case studies - Ligand based design

Week 12 QSAR and case studies

This is a completely new version of CBMS842, run for the first time this year. It has no overlap with any previous offering of CBMS842 and requires CBMS306 (or equivalent) as a prerequisite.