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NES2407 : Applied Computational Medicinal Chemistry

  • Offered for Year: 2024/25
  • Module Leader(s): Dr Agnieszka Bronowska
  • Owning School: Natural and Environmental Sciences
  • Teaching Location: Newcastle City Campus

Your programme is made up of credits, the total differs on programme to programme.

Semester 2 Credit Value: 10
ECTS Credits: 5.0
European Credit Transfer System


• 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

Different levels of theory: strengths and limitations

Molecular mechanics

Factors driving the molecular recognition events

Target structural biology and modelling

Incorporating flexibility: molecular dynamics simulations

Protein “druggability”: binding site search

Molecular docking and virtual screening

Lead optimisation

Modelling covalent and noncovalent inhibitors

Heterobifunctional small molecules: modelling PROTACs

Data analysis

Teaching Methods

Teaching Activities
Category Activity Number Length Student Hours Comment
Guided Independent StudyAssessment preparation and completion11:001:00Formative assessment completion.
Guided Independent StudyAssessment preparation and completion41:004:00Completion of the coursework assignment
Scheduled Learning And Teaching ActivitiesLecture161:0016:00Lectures
Guided Independent StudyAssessment preparation and completion321:0032:00Revision for the final examination
Guided Independent StudyAssessment preparation and completion12:002:00Examination
Scheduled Learning And Teaching ActivitiesPractical102:0020:00Dry Labs (10 practical sessions)
Scheduled Learning And Teaching ActivitiesWorkshops21:002:00Workshops / Case Study seminars
Guided Independent StudyIndependent study123:0023:00Background reading to all topics and practice paper questions
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 Examination1202A50N/A
Other Assessment
Description Semester When Set Percentage Comment
Report2M50Coursework assignment - Dry Lab Report
Formative Assessments

Formative Assessment is an assessment which develops your skills in being assessed, allows for you to receive feedback, and prepares you for being assessed. However, it does not count to your final mark.

Description Semester When Set Comment
Prob solv exercises2MCanvas quizzes.
Assessment Rationale And Relationship

The examination will test the students’ knowledge and understanding of the content of this module in the context of computational structural biology, molecular modelling, and medicinal chemistry. Coursework assessment in the form of lab report will test practical skills acquired in Dry Labs. Formative assessment (Canvas quizzes) will consolidate general concepts and elements of practical skills.

Reading Lists