SFAK24001U Medicinal and Biostructural Chemistry

Volume 2024/2025
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 bioinformatics and structural biology. Genome structure will be introduced focusing primarily on the importance of systematic variations of the human genome in relation to diseases. Sequence alignment will be discussed, and students will get to use internet-based tools for sequence analyses. The course will cover examples of the application of data science methods relevant to drug design. The course will provide basic knowledge about the structure of proteins, including 3D structural information and experimental methods for structure determination. Methods for the design and development of substances - small molecules and biopharmaceuticals, in particular - with specific or selective effects on biochemical or physiological processes will be introduced. Emphasis will be on the significance of steric, stereochemical, conformational, and electrostatic factors for decision-making in drug design. The use of structure-activity relationships (SAR) in drug design will be presented. The importance of changes in structural and physico-chemical parameters in order to obtain drugs with appropriate pharmacokinetic properties will be discussed. Students will be introduced to systems biology, and the importance of protein-protein interactions, and particular emphasis is on peptides and proteins as drugs, including peptidomimetics and peptide and protein design. Examples of structure-based design towards main drug target classes such as receptors, transporters, and enzymes, will be presented and covered in classes and practicals.

 

Learning Outcome

The course objective is to give students insight into the molecular mechanisms of action of selected drugs and to acquaint them with the fundamental principles of drug design and discovery. The course aims to expand student knowledge of the chemical and structural factors relating to the main drug groups and to give examples of the use of chemical principles to clarify the interaction of small molecule or biopharmaceutical drugs with macromolecules in the organism. This includes a basic understanding of the 3D structure of drugs and target macromolecules. Students shall be able to use the vast amount of sequence and biostructural information on relevant target macromolecules available on internet databases, and to use such information about protein primary sequence and 3D structures of macromolecules in the context of drug design.

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

 

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.
  • Use computational tools for structural analysis and machine learning

 

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

  • 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
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)
•10 class lessons as journal clubs (45-minutes)
•4 Four hour computer exercises
  • Category
  • Hours
  • Lectures
  • 31
  • Class Instruction
  • 9
  • Preparation
  • 102
  • Theory exercises
  • 16
  • Guidance
  • 48
  • 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
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

Written on-site exam - 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.

Students are also allowed to bring a molecular model building set.

Marking scale
7-point grading scale
Censorship form
No external censorship
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