Monash University Handbook 2010 Undergraduate - Unit

Level	Undergraduate
Faculty	Faculty of Pharmacy and Pharmaceutical Sciences
Offered	Parkville First semester 2010 (Day)
Coordinator(s)	Dr David Chalmers

Synopsis

This unit provides an introduction to the techniques and applications of molecular modelling with particular emphasis on methods used in drug design. The unit contains two streams:

1. modelling methods; which introduces quantum mechanics, molecular mechanics, energy optimisation and molecular simulation and
2. modelling applications; which covers quantitative structure-activity relationships (QSAR), pharmacophores, structure-based drug design and homology modelling.

This will involve:

• Modelling methods in computational chemistry
• Applications of molecular modelling

Objectives

At the end of this unit students will have:

• A broad understanding of computational chemistry and its application to drug bimolecular problems.
• An understanding of common molecular modelling terminology. - An appreciation of the factors involved in performing quantum mechanical (QM) calculations and the information that these calculations can provide.
• An appreciation of molecular mechanisms energy calculations and the information that these calculations can provide.
• An understanding of the components making up molecular mechanic force fields including bond stretching, angle bending and dihedral angle terms and nonbonded interactions (van der Waals and electrostatic).
• An understanding of molecular potential energy surfaces and the concepts of global and local minima. - An appreciation of energy optimisation methods including steepest descents and conjugate gradient methods.
• An appreciation of approaches to finding global energy minima.
• An understanding of the Boltzmann distribution and the relationship between temperature and the population of energetic states.
• An appreciation of molecular simulation methods.
• An understanding of drug physicochemical properties including electronic, steric and hydrophobic characteristics.
• An understanding of the statistical methods used to develop QSAR equations
• An appreciation of the application of QSAR in drug discovery.
• An appreciation of impact of drug physicochemical parameters on biopharmaceutical properties.
• Un understanding of the pharmacophore concept and its use in drug discovery.
• An appreciation of structure and ligand-based drug design.
• An appreciation of homology modelling methods.
• The ability to use a specific molecular modelling package to study molecular conformation and analyse drug-receptor interactions.
• Describe the molecular interactions which govern molecular structure including bonded, non-bonded and electrostatic interactions.

After completing this unit the student will have the following practical skills:

• Perform simple molecular modeling studies using the molecular modeling package Sybyl.
• Describe the processes involved in molecular mechanics energy calculations.
• Explain the processes involved in running quantum mechanics calculations.
• Interpret and critique a QSAR equation.
• Generate statistically acceptable QSAR equations from physicochemical parameters and biological activity data.
• Derive simple pharmacophore models.
• Describe protein-ligand interactions and how an understanding of these can be applied to drug design.
• Investigate a research topic using literature sources and write a simple report.

Assessment

Final exam (2 hour): 70%; mid-semester exam: 10%; practical assessment: 20%.

Chief examiner(s)

Dr David Chalmers

Contact hours

36 hours of lectures; nine 4 hour practical classes

Prerequisites

PSC1021 Organic Chemistry I
PSC1022 Organic Chemistry II
PSC1041 Mathematics for Pharmaceutical Scientists
PSC1071 Physical Chemistry I
PSC1072 Physical Chemistry II

Additional information on this unit is available from the faculty at:

http://www.monash.edu.au/muso/support/