SLKKIL112U Structure-based Drug Research

Volume 2024/2025
Education

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

 

Content

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
Learning Outcome

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)
If you are applying for the course as a credit transfer student, you must have passed SFAK18003E Medicinal and Biostructural Chemistry or have acquired similar competencies in another course. Documentation for corresponding competencies in the form of a course description and an exam result must be attached to your application.
Teaching is organized on the assumption that students have already acquired knowledge in medicinal and biostructural chemistry, including protein structures, biophysical techniques, protein-ligand interactions, and basic organic and physical chemistry. No special skills for computer programming are needed. Software with graphical user interfaces will be used.
The course will comprise 8 modules, introducing experimental and computational methods with focus on different aspects of structure-based drug research.

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
Continuous feedback during the course of the semester

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.

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

Kandidat i farmaci - 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