Molecular Modelling in the study of foods and drugs
Learning outcomes of the course unit
The course aims to give an overview of the different computational methodologies available to gain insight into the processes of biomolecular recognition, with special emphasis in the thermodynamics and kinetics of ligand-receptor binding and the analysis of structure-activity relationships.
Prerequisites
General concepts of physicochemical properties of (bio)organic compounds, chemical reactivity, and structural biochemistry
Course contents summary
The course will provide an updated overview of the modeling and simulation techniques available for the study of macromolecular components of foods and the interaction of bioactive ligands with macromolecular targets. The course will be focused on the key role played by molecular interactions in regulating the bioactivity of functional (macro)molecules in cellular processes. To this end, a brief overview of the computational techniques available for the analysis of molecular interactions will be made. Attention will then be paid to structure-based techniques, covering both ligand-based and target-based computational approaches. The need to account for dynamical effects in the definition of conformational ensembles will be covered with molecular dynamics simulations. Understanding of the energetics associated with molecular processes will be made through strategies aimed at prediction of free energy changes. Finally, the course will give an overview of advances simulation techniques. The physical rules that underly the different methods will be complemented with representative examples showing the range of potential applications in food sciences, which will be supplemented with practical hands-on sessions.
Molecular interactions and bioactivity.
Database for biomolecular simulation
Methods in molecular modeling and simulation
Ligand-based techniques: QSAR and 3D-QSAR
Docking: Ligand-protein and protein-protein
Molecular dynamics
Free energy calculations
Advanced simulation methods
Recommended readings
Gu, J. and Bourne, P. E. Structural Bioinformatics. 2nd edition. Wiley Blackwell 2009
Luque, F. J., Barril, X Physico-Chemical and Computational Approaches to Drug Discovery.. (eds). RSC Drug Discovery 2012
Gohlke, H. (ed). Wiley VCH Protein-Ligand Interactions. Methods and Principles in Medicinal Chemistry Series, Vol. 53,. Weinheim 2012
Teaching methods
The course will combine lectures and applied classes. Lectures will pursue to introduce the fundamental theoretical concepts of the computational methodologies used in computational biology, but emphasis will be made in the hands-on application through molecular modeling case studies.
Assessment methods and criteria
The final evaluation will be based on the analysis of specific practical cases taken from the literature. It will consist in solving questions related to the key concepts of ligand-receptor interactions from the analysis of illustrative cases of ligand-receptor complexes.
