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
Semesters
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 | |
Aims
• 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 Study | Assessment preparation and completion | 1 | 2:00 | 2:00 | Examination |
| Guided Independent Study | Assessment preparation and completion | 1 | 1:00 | 1:00 | Formative assessment completion. |
| Guided Independent Study | Assessment preparation and completion | 4 | 1:00 | 4:00 | Completion of the coursework assignment |
| Scheduled Learning And Teaching Activities | Lecture | 16 | 1:00 | 16:00 | Lectures |
| Guided Independent Study | Assessment preparation and completion | 32 | 1:00 | 32:00 | Revision for the final examination |
| Scheduled Learning And Teaching Activities | Practical | 10 | 2:00 | 20:00 | Dry Labs (10 practical sessions) |
| Scheduled Learning And Teaching Activities | Workshops | 2 | 1:00 | 2:00 | Workshops / Case Study seminars |
| Guided Independent Study | Independent study | 1 | 23:00 | 23:00 | Background reading to all topics and practice paper questions |
| Total | 100:00 |
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
Exams
| Description | Length | Semester | When Set | Percentage | Comment |
|---|---|---|---|---|---|
| Written Examination | 120 | 2 | A | 50 | N/A |
Other Assessment
| Description | Semester | When Set | Percentage | Comment |
|---|---|---|---|---|
| Report | 2 | M | 50 | Coursework 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 exercises | 2 | M | Canvas 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
Timetable
- Timetable Website: www.ncl.ac.uk/timetable/
- NES2407's Timetable