Quantitative chemical structure and activity relationship

1. Complementarity between in vitro, in vivo and in silico approaches in toxicology
2. Potential energy
3. Proteins as complex systems
4. Competitive and non-competitive inhibition
5. Binding affinity and equilibrium dissociation constant (Kd)
6. Introduction to molecular modelling
7. Hints of computational quantum mechanics
8. Molecular mechanics
9. Molecular docking
10. Pharmacodynamics of xenobiotics and evaluation of their toxic effects
11. The target (and off-target) problem
12. Methods to predict target proteins for toxic agents on a proteome-wide scale (Virtual screening of large protein databases)
13. Structure-based versus ligand-based toxicity prediction approaches
14. Species cross-transferability analysis; reduction and optimization of animal testing

Classroom activity (4 CFU)
1. Introduction to bioinformatics
2. Genome organization and evolution
3. Databases, archives and information retrieval
4. Substitution matrices, pairwise and multiple alignments, database search and phylogenetic trees
5. Protein structure and architecture
6. Protein structure prediction and validation: comparative modelling, threading and ab initio approaches
7. Case studies: chimeric comparative modelling of a receptor/target; distant homology modelling of an enzyme
8. Xenobiotic and novel drug risk assessment and prioritization
9. Case study: evaluation of endocrine active substances through an efficient in silico pipeline
10. Introduction to systems biology

Bioinformatics laboratories (1 CFU)
1. Building small molecules, biopolymers and introducing their PTMs
2. Protein comparative modelling
3. Molecular docking
4. Quantitative structure-activity relationship in practice