Concepts in Chemical Biology

Course manual 2025/2026

Course content

Apart from a general introduction, four main topics are discussed, introducing different techniques central to Chemical Biology research:

1) Chemical Glycobiology

2) Virus Biology and Inhibition

3) Targeting Hallmarks of Cancer

4) Chemical Protein Engineering

Recommended background knowledge: basic physico-chemical knowledge: e.g. Gibbs free energy, forces (coulomb, H-bonds, van der Waals), - basic chemical knowledge: e.g. electronegativity, bond character, acids & bases, organic synthesis - basic biochemical knowledge: e.g. general characteristics of a bacterial, mammalian and plant cell, phospholipids & biological membrane formation and function, nucleotides, DNA, RNA, double helix formation, gene regulation, amino acids and peptide bond formation, protein primary, secondary and tertiary structure, transcription, translation, post-translational modifications, signal transduction, principle of enzymatic reactions.

Objectives

• Students will attain the ability to critically discuss published data.
• After the course, students are expected to know the hallmarks of cancer and know the underlying principles.
• After the course, students are expected to know core cancer signaling pathways.
• After the course, students are expected to know inhibition strategies of signaling pathways – e.g. use of small molecules, stabilized peptides.
• After the course, students are expected to know peptidomimetics and their use for challenging targets in signaling pathways.
• After the course, students are expected to know chemical reactions for the selective covalent modification of proteins.
• After the course, students are expected to know protein labeling techniques (encoded tags, enzymes (PTMs), reactions).
• After the course, students are expected to know bio-orthogonal and ligand directed reactions.
• After the course, students are expected to know (non-)natural protein modifications for improved functions.
• After the course, students are expected to know classical protein engineering (natural: directed evolution, disulfide…).
• After the course, students are expected to know principles of coronavirus infections.
• After the course, students are expected to know the basics of coronavirus targeting approaches.

Teaching methods

• Self-study
• Lecture
• Seminar

The teaching methods for this course:

1)  Lectures: Lectures will be given in English, and their content as well as the associated literature are preparation for the assignments.

2) Case Study and Assignment: The students are provided with one or more research papers. Alone or in groups of two, questions regarding these case studies are addressed in an assignment.

3) Guided Peer-to-Peer Discussions: In seminar sessions, Peer-to-Peer exchange for each topic will take place. Within these, the students are expected to exchange questions and help each other in answering these. Students are expected to participate actively. Discussions should be held in English and also be joined by one of the lecturers.

Learning activities

Attendance

This programme does not have requirements concerning attendance (TER part B).

Assessment

Students who have handed in all four assignments can participate in the final exam. The course grade will only be based on the grade of the exam.

Fraud and plagiarism

The 'Regulations governing fraud and plagiarism for UvA students' applies to this course. This will be monitored carefully. Upon suspicion of fraud or plagiarism the Examinations Board of the programme will be informed. For the 'Regulations governing fraud and plagiarism for UvA students' see: www.student.uva.nl

Course structure

Contact information

Coordinator

• I. Drienovska PhD

Staff