CHY8825 : Proteins as Drug Targets: structure, function, and molecular modelling

Semester 1 Credit Value: 10
ECTS Credits: 5.0


The purpose of this course is to equip students with solid foundations in structural biology, protein biochemistry, and proteins as drug targets – from principles governing protein structure and dynamics, drug-protein interactions, through pharmacology, to modern methods in protein structure prediction and protein simulations. This will be organised in two thematic blocks.

The first one will focus on key concepts of molecular pharmacology and elements of protein biochemistry, cell and molecular biology, relevant in the context of modern drug chemistry. Students will learn about relationships between ligand-receptor interactions and protein structure, signal transduction in relationship to the cell anatomy and fundamental biochemistry, and molecular pharmacology of different classes of receptors, ion channels, and enzymes. Students will also learn about the methodology of preclinical studies and clinical trials. Additionally, students learn about the pharmacology of CNS, cardiovascular, and immune systems, linking physiology, cell biology, biochemistry, molecular pharmacology, and medicinal chemistry.

The second block is intended to make students familiar with the basic terminology, key concepts, data formats and algorithms of modern protein modelling and simulation methods. This will include structure prediction using homology and ab initio protein modelling, building protein-ligand and protein-protein complexes and fitting the atomistic data to lower-resolution sets. The students will be taught about the establishment of intellectual property through modelling techniques. During this part of the course, students will also learn techniques suitable for visualising macromolecular data using the open-source as well as proprietary software packages.

Outline Of Syllabus

Introduction to macromolecules, drug-receptor interactions and molecular pharmacology
Dr. Agnieszka K. Bronowska

• Key elements of biochemistry: proteins, peptides, nucleic acids, lipids, and small molecules
• Important metabolic pathways
• Foundations of cell biology: anatomy of the cell, structure and functions of cellular organellae and their compartments
• Receptor-ligand interactions and protein structure
• Principles of thermodynamics in drug chemistry context
• Signal transduction and modulation
• Pharmacokinetics and pharmacodynamics
• Molecular pharmacology of receptors, channels and enzymes
• Pharmacology of the central nervous system
• Pharmacology of the cardiovascular system
• Pharmacology of the immune system: molecular basis of inflammation
• Before the molecule becomes a drug: methods in preclinical studies
• An overview of clinical trials
• Case Studies 1

Introduction to macromolecular modelling
Dr. Agnieszka K. Bronowska

• Key concepts, tools and techniques
• Data banks and data formats
• Modelling of proteins and nucleic acids
• Sequence alignments and sequence homology
• Homology modelling
• De novo modelling
• Building macro-complexes
• Fitting atomistic detail to lower-resolution datasets
• Ligands: peptides, peptidomimetics, and small organic molecules
• Aiding the establishment of intellectual property through modelling techniques
• Case Studies 2
• Visualisation of macromolecules: types of data and how to represent them. Software used in macromolecular data visualisation. Formats. Vector and raster graphics. Image resolution.

Teaching Methods

Teaching Activities
Category Activity Number Length Student Hours Comment
Guided Independent StudyAssessment preparation and completion12:002:00Final examination
Guided Independent StudyAssessment preparation and completion111:3011:30Revision for final exam
Guided Independent StudyAssessment preparation and completion53:0015:00Writing up of dry lab reports
Scheduled Learning And Teaching ActivitiesLecture151:0015:00N/A
Scheduled Learning And Teaching ActivitiesPractical52:0010:00Dry labs
Scheduled Learning And Teaching ActivitiesWorkshops21:002:00one workshop for each thematic band
Guided Independent StudyIndependent study129:3029:30Background reading and practice exam questions
Guided Independent StudyIndependent study115:0015:00Skills practice
Teaching Rationale And Relationship


Assessment Methods

The format of resits will be determined by the Board of Examiners

Description Length Semester When Set Percentage Comment
Written Examination1201A60N/A
Other Assessment
Description Semester When Set Percentage Comment
Written exercise1M40Assessment of practical work performed in dry labs
Assessment Rationale And Relationship

The examination will test the student’s knowledge and understanding of the coursework. The in course assessment will test information literacy and presentation skills.

Study Abroad students may request to take their exam before the semester 1 exam period, in which case the format of the paper may differ from that shown in the MOF. Study Abroad students should contact the school to discuss this.

Reading Lists