SLKKIL112U Structure-based Drug Research
MSc Programme in Medicinal Chemistry - compulsory
MSc Programme in Pharmacy (Danish programme cand.pharm) - elective
MSc Programme in Pharmaceutical Sciences (Danish programme cand.scient.pharm) - restricted elective
MSc Programme in Pharmaceutical Sciences (English programme) - restricted elective
In modern drug research the focus is on analysis and optimization of the interactions between the drug and the specific target. This course focuses on essential experimental and computational methods for analyses of target proteins and their interactions with drugs or drug-like molecules.
The course is divided into eight modules introducing different
methods and how to use the results in structure-based drug design
of small molecules and biopharmaceuticals. In the lectures, the
students are introduced to the fundamental principles behind the
methods and exercises will provide the students with hands-on
experience with e.g. data processing or analysis.
The course will cover the following:
- Modelling and engineering of target proteins
- Protein structure determination using X-ray crystallography and single particle electron microscopy
- Analysis of protein targets and their formulation in solution using small angle X-ray scattering (SAXS)
- Creation and use of ligand-based pharmacophore models in drug design for the identification of potential ligands
- Identification of potential ligands/drug candidates through docking of small molecules into the binding site of the protein target
- Analysis of interactions between protein targets and small molecule drugs/biopharmaceuticals for structure-based drug design
- Assessing the similarity of small molecules and performing ligand-based virtual screening in support of structure-based drug research
This course is relevant for students interested in the drug research area and other areas where it is important to:
- have knowledge about experimental and theoretical methods that can be used to analyze molecular characteristics of biologically important molecules
- understand the interactions between ligands and biomacromolecules
- get hands-on experience with modern tools in experimental and theoretical molecular modeling
The course objective is to provide the students with knowledge and competences within experimental and computational methods for structure-based drug research. This includes analyses of small molecule drugs and biopharmaceuticals, as well as their interactions with relevant target proteins.
At the end of the course, students will be able to:
Knowledge
- know the key concepts of interactions between protein targets and small molecule drugs/biopharmaceuticals
- know the principles and methods used for rational design of drugs
- understand requirements, advantages and limitations of the methods used in structure-based drug design
Skills
- analyse and evaluate data from methods in experimental structure analysis (protein crystallography, SAXS, electron microscopy)
- extract relevant information from 3D structural models (experimental or theoretical)
- apply and evaluate computer-based tools in modern drug research (e.g. pharmacophore modelling, ligand docking, virtual screening)
Competences
- select the most appropriate experimental method and computer-based tools for drug design and discovery
- use and critically evaluate results achieved from experimental structural analyses of proteins and drugs
- use and critically evaluate results obtained with computer-based methods for structure-based discovery and design of drugs
- Reviews and scientific papers available at the course homepage
- Supplementary notes (notes with additional information on methods used – to be downloaded from course homepage)
The structure for a module will be:
Monday: 1 introductory lecture
Wednesday: 2 lectures + exercises
Monday (following week): Student presentations and summarizing wrap-up
From Monday to Wednesday, the students can prepare for the upcoming exercises. Wednesday to Monday, the students are expected to finalize exercise work and to prepare for the presentations Monday afternoon.
• Lectures: 24 hours
• Computer exercises: 40 hours
• Student presentations: 24 hours
• Preparation: 115 hours
• Exam: 3 hours
Total: 206 hours
- Category
- Hours
- Lectures
- 24
- Preparation
- 115
- Exercises
- 40
- Project work
- 24
- Exam
- 3
- Total
- 206
Exercises: Each exercise module will be concluded with selected student presentations with feedback and discussion.
Lectures: Digital quizzes are used as a supplement to the modules.
Open for credit transfer students and other external students. Apply here:
Credit transfer students:
Credit transfer student at SUND – University of Copenhagen
(ku.dk)
Other external students:
http://healthsciences.ku.dk/education/exchange_guest_students/guest-students/
Credit transfer and other external students are welcomed on the course if there are seats available and they have the academic qualifications.
- Credit
- 7,5 ECTS
- Type of assessment
- On-site written exam, 3 hours under invigilation
- Type of assessment details
- The examination consists of assignments in a multiple choice format. For each assignment at least three possible answers are provided. The assignments cover the topics of the course ranging from experimental structure determination to computational methods.
- Aid
- Written aids allowed
Find more information about written on-site exams in the exam rooms, incl. information about standard programs on the exam PCs at KUnet
In addition to the standard programs digital notes are permitted for this exam. It is allowed to upload notes for the ITX exam via digital exam. You will find a link to this feature from your exam in Digital Exam.
- Marking scale
- 7-point grading scale
- Censorship form
- No external censorship
- Re-exam
10 or fewer students registered for reexam:
Type of assessment: Oral examination
Assessment details: 30 minutes examination
Preparation: None
Aids: Written aids
Criteria for exam assesment
To achieve the grade 12 the student must be able to:
Knowledge
- know the key concepts of interactions between protein targets and small molecule drugs/biopharmaceuticals
- know the principles and methods used for rational design of drugs
- understand requirements, advantages and limitations of the methods used in structure-based drug design
Skills
- analyse and evaluate data from methods in experimental structure analysis (protein crystallography, SAXS, electron microscopy)
- extract relevant information from 3D structural models (experimental or theoretical)
- apply and evaluate computer-based tools in modern drug research (e.g. pharmacophore modelling, ligand docking, virtual screening)
Competences
- select the most appropriate experimental method and computer-based tools for drug design and discovery
- use and critically evaluate results achieved from experimental structural analyses of proteins and drugs
- use and critically evaluate results obtained with computer-based methods for structure-based discovery and design of drugs
Course information
- Language
- English
- Course code
- SLKKIL112U
- Credit
- 7,5 ECTS
- Level
- Full Degree MasterFull Degree Master choice
- Duration
- 1 block
- Placement
- Block 4
- Schedule
- C
- Course capacity
- 54 students
Study board
- Study Board of Pharmaceutical Sciences
Contracting department
- Department of Drug Design and Pharmacology
Contracting faculty
- Faculty of Health and Medical Sciences
Course Coordinators
- Karla Andrea Frydenvang (16-746a7b756a376f7b826d6e777f6a7770497c7e776d37747e376d74)
- Annette Eva Langkilde (17-6b78786f7e7e6f38766b78717573766e6f4a7d7f786e38757f386e75)
- Albert J. Kooistra (15-69746a6d7a7c36737777717b7c7a69487b7d766c36737d366c73)