SFAK24001U Medicinal and Biostructural Chemistry

Volume 2025/2026
Education

MSc Programme in Pharmacy and Pharmaceutical Sciences (Danish study programs for cand.pharm. and cand.scient.pharm.) - compulsory

MSc Programme in Medicinal Chemistry - compulsory

MSc Programme in Pharmaceutical Sciences (English programme) - compulsory

Content

The course deals with the most important principles of drug design and discovery of small molecules and biopharmaceuticals, including fundamental aspects of molecular biology, bioinformatics, structural biology and data science. The human genome will be introduced focusing primarily on the importance of genetic variations in relation to diseases and drug response variability. Sequence alignment will be discussed, and web-based tools for sequence analyses will be introduced. The course will provide basic knowledge about the structure of proteins, including 3D structural information and experimental methods for structure determination. The course will also introduce systems biology, with emphasis on target validation.  

Methods for the design, characterization and development of substances - small molecules and biopharmaceuticals - with specific or selective effects on biochemical or physiological processes will be introduced. The importance of changes in structural and physico-chemical parameters to obtain drugs with appropriate pharmacokinetic properties will be discussed. Subsequent translational and innovation measures will be introduced. Examples of studies of main drug target classes such as receptors, transporters, and enzymes, will be given. By the end of the course the students will have a comprehensive understanding of the principles and techniques essential for drug discovery and development.

Learning Outcome

The course objective is to give students insight into the early elements of drug design with emphasis on the use of computational methods and the 3-dimensional structures of drug target molecules.

 

At the end of the course, students are expected to be able to:

 

Knowledge:

  • Understand the fundamental principles of drug design and discovery for small molecules, biopharmaceuticals, and new modalities including implications for commercialization.
  • Acquire basic knowledge of molecular biology, bioinformatics, structural biology, and data science relevant to drug discovery.
  • Recognize the significance of the human genome, particularly genetic variations and their role in disease and drug response variability.
  • Comprehend the 3D structure and function of proteins, including methods for structural determination and functional characterization.
  • Understand the principles of systems biology, focusing on target validation in drug development.
  • Grasp the role of structural and physico-chemical parameters in developing drugs with suitable pharmacodynamic and pharmacokinetic properties.

 

  Skills:

  • Analyse gene and protein sequence variability, using classical and web-based sequence alignment approaches.
  • Analyse 3D structural information of proteins using relevant protein structure visualization tools.
  • Evaluate ligand-protein interactions for key drug targets using computational tools.
  • Apply and interpret basic AI and machine learning approaches in a Python Programming language environment for drug target ligand identification.
  • Independently plan and prepare presentations of published research.
  • Critically assess literature studies related to drug discovery and design.

 Competences:

  • Independently plan and prepare presentations of published research.
  • Identify and validate drug targets using approaches from systems and molecular biology.
  • Design structure-based strategies to optimize binding and physico-chemical properties of drug candidates.
  • Collaborate in research settings to conduct drug design and development processes.
  • Communicate complex scientific concepts related to drug discovery to both specialised and general targeted audiences.

  • The Handbook of Medicinal Chemistry: Principles and Practice. Ward, Simon E; Davis, Andrew (Eds.), 2th Edition, 2023, The Royal Society of Chemistry England

  • Biochemistry. Jeremy M. Berg, John L. Tymoczo and Lubert Stryer, 10th edition, 2023

  • Scientific papers and reviews available at the course website
None.
Course teaching is based on the assumption that students have previous knowledge from basic courses in organic chemistry, physical chemistry, biochemistry, and general pharmacology, preferably corresponding to the content of the compulsory courses on these topics in the BSc in Pharmacy programme. Special IT knowledge is not a requirement, but all students need to bring a laptop computer for the computer exercises.
•31 lectures (45-minutes)
•9 class lessons as journal clubs (45-minutes)
•4 Four hour computer exercises
  • Category
  • Hours
  • Lectures
  • 31
  • Class Instruction
  • 9
  • Preparation
  • 150
  • Theory exercises
  • 16
  • Total
  • 206
Continuous feedback during the course of the semester

Feedback is given to student presentations in class lessons, which are conducted in a 'journal club' format.

Credit
7,5 ECTS
Type of assessment
On-site written exam, 3 hours under invigilation
Type of assessment details
Individual 3-hour written examination.
Examination design:
The examination assignment typically consists of 3 assignments each with 5 sub-assignments. For each sub-assignment, at least 3 possible answers are provided in a multiple-choice format. Typically one of the 3 assignments deals with biostructural aspects, whereas the remaining two assignments are more medicinal chemistry focused.
Aid
Only certain aids allowed (see description below)

In addition to the standard programs, written aids, digital notes and molecule model building set 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.

Find more information about written on-site exams in the exam rooms, incl. information about standard programs on the exam PCs at KUnet

Written on-site exam - KUnet

 

 

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: 20 minutes examination

Preparation: 30 minutes

Aids: All aids allowed

Criteria for exam assesment

To achieve the grade 12 the student must have:

 

Knowledge

  • Know the concepts used to describe molecular interactions in the context of drug design and discovery
  • Be able to explain the principles of small molecules and biopharmaceutical drug actions on a number of biological targets
  • Know the basic concepts from bioinformatics used in drug design and discovery
  • Can understand, reflect, explain, and critically evaluate molecular interactions in the context of drug design and discovery
  • Can understand, reflect, explain, and critically evaluate the principles of drug actions on a number of biological targets
  • Can understand, reflect and critically evaluate results from bioinformatics in drug design and discovery
  • Basic knowledge on how machine learning can be used in drug design

 

Skills 

  • Master, discuss and evaluate the use of 3D structures in ligand design
  • Master, discuss and evaluate the use of the information available from sequenced genomes to solve problems related to drug design and discovery
  • Master, discuss and evaluate the use of pharmacophores in drug design
  • Master, discuss and evaluate the use of basic methodologies of receptor pharmacology in drug design
  • Discuss and evaluate fundamental principles of peptide and protein design
  • Assess, evaluate, independently discuss and present published research related to drug design and discovery.

 

Competences

  • Independently plan and prepare presentations of published research
  • Implement the use of the relationship between chemical structure and biological activity of important drug classes
  • Take responsibility for and coordinate presentations of published research related to drug design and discovery
  • Implement and develop further the use of 3D structures in ligand design
  • Implement and develop further the use of the relationship between chemical structure and biological activity of important drug classes