Structural and Computational Medicinal Chemistry

Course content

The course focuses on molecular modelling techniques and their use in modern drug research, illustrated through lectures, exercises, and project work. In the lectures, the students are introduced to the fundamental principles behind the methods in molecular modeling. In the exercises, the students get hands-on experience with modern computer-based tools, and the project work gives the opportunity to apply these tools on a drug targets with the aim of understanding and improving the binding to a protein target.

The methods covered in the lectures, exercises, and project work are:

  • investigating bioactive conformations of drug-like molecules
  • analyzing molecular characteristics of ligands and protein binding sites
  • structure-based drug design and ligand-based drug design
  • pharmacophore development and quantitative structure activity relationships (QSAR)
  • homology modelling
  • docking of ligands into the binding pocket of the target protein.
  • investigating protein-protein interfaces relevant for biopharmaceutics

 

Objective

The course is relevant for research within the drug discovery 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 molecular modeling to achieve skills to develop new compounds
Education

MSc Programme in Medicinal Chemistry - compulsory

MSc Programme in Pharmacy or Pharmaceutical Sciences (Danish programmes cand.pharm and cand.scient.pharm) - elective

MSc Programme in Pharmaceutical Sciences (English programme) - elective

 

Learning outcome

At the end of the course, students will be able to:

 

Knowledge

  • explain the characteristics that influence the relationship between molecular structure and biological activity
  • be critical to the principles and methods used for rational discovery and development of new or better drugs

 

Skills

  • use and critically evaluate results achieved from structure determination of proteins and drug-related compounds
  • use and critically evaluate results obtained with modern computer-based methods for structure-activity analysis of biologically active compounds
  • have hands-on experience with modern tools in molecular modeling.

 

Competences

  • plan a computer-based project on how to improve binding to a target
  • apply the computer-based tools for projects in drug discovery
  • select the appropriate molecular modelling techniques in modern drug research

Lectures: 19 hours
•Computer exercises: 18 hours
•Project work: 78 hours
•Supervision during project work: guidelines will be available on the course homepage
•Exam: 0,5 hours

  • Reviews and scientific papers available at the course website
  • Supplementary notes (notes with additional information on methods used – to be downloaded from course homepage)

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 graphic user interfaces will be used.

ECTS
7,5 ECTS
Type of assessment
Oral examination, 30 min
Individual 30 minutes oral exam (assessment included) with a presentation of project work (based on the poster) as starting point for the exam, followed by an examination in the methods presented and used during the course, i.e. all the written course material. The student is expected to present:
- detailed knowledge of specified topics in the course material,
- basic knowledge of the rest of the course material, and
- detailed knowledge of own project
Aid
All aids allowed
Marking scale
7-point grading scale
Censorship form
No external censorship
Criteria for exam assessment

To achieve the grade 12 the student must be able to:

Knowledge

  • explain the characteristics that influence the relationship between molecular structure and biological activity
  • be critical to the principles and methods used for rational discovery and development of new or better drugs

 

Skills

  • be able to use and critically evaluate results achieved from structure determination of proteins and drug-related compounds
  • be able to use and critically evaluate results obtained with modern computer-based methods for structure-activity analysis of biologically active compounds
  • have hands-on experience with modern tools in molecular modeling.

 

Competences

  • plan a computer-based project on how to improve binding to a target
  • apply the computer-based tools for projects in drug discovery
  • select the appropriate molecular modelling techniques in modern drug research

Single subject courses (day)

  • Category
  • Hours
  • Lectures
  • 19
  • Theory exercises
  • 18
  • Preparation
  • 70
  • Project work
  • 78
  • Exam
  • 21
  • English
  • 206