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The University of Southampton

NATS3006 Drugs of the future: designing a magic bullet

Module Overview

Aims and Objectives

Module Aims

The rational design of protein inhibitors brings together knowledge of physical chemistry, synthetic organic chemistry, molecular modelling, structural biology, enzymology/protein biochemistry and pharmacology. The overall aim of this module is to equip our students with the basic factual knowledge that, together with knowledge acquisition skills and critical thinking skills, will enable them to understand the processes that are involved in the rational design of protein inhibitors. The core of the course will provide an integrated approach to the processes of designing and synthesising a specific protein inhibitor.

Learning Outcomes

Learning Outcomes

Having successfully completed this module you will be able to:

  • the ability to access and interrogate protein structure databases
  • a good understanding of how to design an inhibitor matched to a given active site structure
  • a conceptual understanding of the chemical synthesis of an inhibitor
  • practical skills in the chemical synthesis of an inhibitor
  • a critical understanding of protein-inhibitor binding kinetics and thermodynamics
  • practical skills in determining protein-inhibitor binding kinetics
  • the ability to determine the effectiveness of a new inhibitor
  • a broad and critical understanding of the advantages and limitations of using a structure-driven approach to drug design
  • strategies for acquiring, collating, interpreting, evaluating and presenting complex technical information from cutting-edge research publications


The philosophy underlying this course is to empower students to take charge of their own learning in the area of rational drug design. As a consequence the course will make extensive use of directed and peer-assisted self-learning methods. The module will be delivered in the context of designing, synthesising and evaluating a small-molecule inhibitor of a target protein. Three main areas will be addressed: structural biology & databases, molecular modelling, pharmacokinetics and inhibitor design. Structural biology & databases Topics include: crystallographic 3D structure determination; accessing and retrieving protein structural data; active site structure determination Molecular modelling Topics include: fundamentals of molecular dynamics simulations; docking; estimating binding energies; visualising structure using Pymol. Pharmacokinetics Topics include: enzyme kinetics; enzyme inhibitors; ligand-receptor binding kinetics; IC50 and dose responses. Inhibitor design Topics include: carbohydrate inhibitors; carbohydrate synthesis

Learning and Teaching

Independent Study100
Practical classes and workshops20
Total study time150



MethodPercentage contribution
Assessment 70%
Research proposal 30%
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