Biochemistry applied to the rational design of biologically active molecules

A.A. 2015/2016
Insegnamento per
Crediti massimi
Ore totali
Obiettivi formativi
This course mainly aims to provide (i) the theoretical bases for the understanding of drug development approaches exploiting structural and functional information on the target proteins and (ii) the tools for designing and testing of putative biologically active molecules. Thus, the course is ideally linked to that on "Advanced chemical methods in biotechnology", especially part 2, while some aspects of structural biology will be further expanded in the "Structural Proteomics" elective class.
Part 1 (Structural biology) will focus on protein structures and techniques for structure-based drug design and screening, while part 2 (Enzymology) will present the tools of mechanistic enzymology used for testing and designing biologically active molecules.
As an added value, this class will provide knowledge and tools to study structure-function relations of proteins, which are needed to elucidate biological processes, for protein engineering and all sound biotechnological applications of proteins.

Struttura insegnamento e programma

Edizione attiva
Esercitazioni: 16 ore
Lezioni: 32 ore
Structural Biology (2 CFU)
- Introduction to the identification of drug molecular targets by bioinformatic, genomic, transcriptomic, and proteomic techniques. Criteria for the validation of pharmacological targets.
- Techniques and strategies for the overexpression and purification of molecular targets, especially proteins and enzymes.
- Review of information on the covalent structure of proteins, their three-dimensional architectures and the factors that stabilize their native conformation. Protein modules and classification of globular proteins. Subunit-subunit interactions. Structure-sequence correlation: homology modelling. Protein stability and flexibility.
- Molecular recognition, localization and nature of ligand binding sites. Structure-function relationships for enzymes: active site geometry, proximity factor and destabilization of the fundamental state, stabilization of the transition state and water exclusion. Strategies for the identification of catalytic residues and of interaction sites with ligands and effectors (docking techniques). Structural basis of enzyme inhibition. Examples.

Enzymology (3 CFU)
- Principles of chemical and enzyme catalysis.
- Design of robust enzyme activity assays for the dissection of enzyme kinetic mechanisms and testing of putative effectors (activators/inhibitors).
- Kinetic approaches to dissect enzyme chemical and catalytic mechanisms
- Classes of active site inhibitors and inactivators and kinetic methods to determine inhibition mechanisms and inhibitors' potency.
Concepts and their applications will be illustrated with examples taken from the literature.
Informazioni sul programma
Copies of the slides projected in the classroom, as well as other materials, will be made available through the course website on the ARIEL platform of the University of Milano ( By no means this material replaces the lectures or reference textbook. The material is made available only to registered students of the Degree Course in Molecular Biotechnology and Bioinformatics and should not be distributed to others.
Prerequisiti e modalità di esame
Recommended Prerequisites
A revision of the topics covered by the basic biochemistry class included in the bachelor curriculum prior to attending the class is highly recommended.

Examination procedures
Written examination with open-answer questions spanning all topics covered in the course.
Metodi didattici
Teaching Mode: Classroom lectures supported by projected material with common discussions on experimental design, data analysis and specific case studies.
Attendance: highly recommended.
Materiale didattico e bibliografia
· Voet, D. & Voet, J.G Biochemistry , 4th Edition, J. Wiley & Sons
· Fersht, A. Structure and mechanism in protein science (Freeman)
· Frey, P.A. & Hegeman, A.D. Enzymatic Reaction Mechanisms, Oxford University Press (2007)
· Petsko, G.A. & Ringe, D. Protein structure and function, New Science Press, 2004
Secondo semestre
Secondo semestre
Modalità di valutazione
Giudizio di valutazione
voto verbalizzato in trentesimi
Giovedi, ore 10:30-12:30
Dip. di Bioscienze, Torre C, 5 piano
Lunedi' ore 13-14
Unita' di Biochimica delle proteine, Edifici Biologici, Via Celoria 26, 5C