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CHY2611 : Applied Computational Medicinal Chemistry

  • Offered for Year: 2022/23
  • Module Leader(s): Dr Agnieszka Bronowska
  • Lecturer: Dr Cristina Navarro Reguero
  • Owning School: Natural and Environmental Sciences
  • Teaching Location: Newcastle City Campus
Semester 2 Credit Value: 10
ECTS Credits: 5.0


By the end of this module students will have an:

• Understanding of requirements for appropriate modelling of macromolecules and their complexes;
• Understanding the fundaments of chemical thermodynamics in the context of drug-protein interactions;
• Awareness of the factors that influence binding affinity of the compounds;
• Awareness of the factors that influence drug-likeness of the compounds and methods able to predict
and optimise these parameters;
• Understanding the techniques used in computational medicinal chemistry and key approximations
behind them;
• Understanding the data analysis techniques in computational medicinal chemistry and different
data formats;

Outline Of Syllabus

Applied Computational Medicinal Chemistry

Different levels of theory: strengths and limitations
Molecular mechanics
Factors driving the molecular recognition events
Target structural biology and modelling
Protein “druggability”: binding site search
Molecular docking and virtual screening
Lead optimisation
Modelling covalent and noncovalent inhibitors
Chemical space screening
Incorporating flexibility: molecular dynamics simulations
Data analysis

Teaching Methods

Teaching Activities
Category Activity Number Length Student Hours Comment
Guided Independent StudyAssessment preparation and completion12:002:00End of module examination
Guided Independent StudyAssessment preparation and completion160:308:00Revision for the final examination
Scheduled Learning And Teaching ActivitiesLecture161:0016:00Lectures
Scheduled Learning And Teaching ActivitiesPractical62:0012:00Dry Labs (6 practical sessions)
Guided Independent StudyDirected research and reading41:004:00Coursework assignments
Scheduled Learning And Teaching ActivitiesWorkshops21:002:00Workshops / Case Study seminars
Scheduled Learning And Teaching ActivitiesDrop-in/surgery111:0011:00Office hour drop in sessions
Guided Independent StudyIndependent study145:0045:00Background reading
Teaching Rationale And Relationship

In lectures students learn concepts in computational medicinal chemistry, encompassing methodology and applications. The case study sessions consolidate these concepts, and practical sessions (Dry Labs) implement those techniques to particular problems.

Assessment Methods

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

Description Length Semester When Set Percentage Comment
Written Examination1202A100Written examination or online assessment as alternative in the case of no PiP examinations
Assessment Rationale And Relationship

The examination will test the students’ knowledge and understanding of the content of this module in the context of both synthetic and mechanistic chemistry. Practical reports in the form of coursework will be set in Semesters 2.

Reading Lists