Quantitative chemical structure and activity relationship

A.A. 2017/2018
Insegnamento per
10
Crediti massimi
88
Ore totali
SSD
BIO/10 CHIM/08
Lingua
Inglese

Struttura insegnamento e programma

Edizione attiva
Responsabile
Moduli o unità didattiche
Methods of analysis applied to water, air, biological fluids, tissues, food and In Silico Methods in Toxicology
CHIM/08 - CHIMICA FARMACEUTICA - CFU: 5
Lectures: 40 ore

Structural Bioinformatics
BIO/10 - BIOCHIMICA - CFU: 5
Laboratory individual activity: 16 ore
Lectures: 32 ore
Docenti: Eberini Ivano, Parravicini Chiara

Prerequisiti e modalità di esame
The course requires the knowledge of basic notions of mathematics, chemistry, biochemistry and molecular biology, which are needed for a proficient comprehension of the lessons. The examination consists of an oral discussion concerning two distinct topics concerning the Structural bioinformatics module and two distinct topics concerning the Methods of analysis applied to water, air, biological fluids, tissues, food and in silico methods in toxicology module.
Methods of analysis applied to water, air, biological fluids, tissues, food and In Silico Methods in Toxicology
Programma
1. Introduction
2. Complementarity between experimental and in silico approaches in toxicology
3. Atomic and molecular orbitals, molecular geometries, molecular properties
4. Molecular modelling
5. Hints of computational quantum mechanics (ab initio methods)
6. Empirical and ab initio force fields models: molecular mechanics
7. Native 3D-structure of a protein: protein folding
8. Molecular dynamics simulations
9. Enhanced conformational sampling of molecular systems
10. Molecular recognition phenomena
11. Binding affinity and equilibrium dissociation constant Kd
12. Molecular docking simulations and its applications in toxicology
13. Methods to predict target proteins for toxic agents on a proteome-wide scale
14. Quantitative Structure-Activity Relationships (QSAR)
15. Artificial Intelligence (AI) and data mining for toxicity prediction
Materiale didattico e bibliografia
· Arthur M. Lesk, Introduction to Bioinformatics, Fourth Edition. Oxford University Press 2014
· Stefano Pascarella, Alessandro Paiardini, Bioinformatica - Dalla sequenza alla struttura delle proteine. Zanichelli 2011
· Andrew R. Leach, Molecular Modelling: Principles and Applications. Pearson - Prentice Hall 2001
Structural Bioinformatics
Programma
Structural Bioinformatics (5 CFU)
Classroom activity (4 CFU)
1. Introduction
2. Genome organization and evolution
3. Scientific publications and archives: media, content and access
4. Archives and information retrieval
5. Alignments and phylogenetic trees
6. Structural bioinformatics, xenobiotics and drug discovery
7. Introduction to systems biology
8. Metabolic pathways
9. Gene expression and regulation

Bioinformatics laboratories (1 CFU)
1. Dot-plot matrices and sequence alignment
2. Building small molecules, biopolymers and introducing their PTMs
3. Protein comparative modelling
4. Molecular docking
5. Quantitative structure-activity relationship in practice
6. Structure-based chemical design tutorial
7. Structural studies on a model protein
8. Protein design: mutant generation and their biophysical properties
Materiale didattico e bibliografia
· Arthur M. Lesk, Introduction to Bioinformatics, Fourth Edition. Oxford University Press 2014
· Stefano Pascarella, Alessandro Paiardini, Bioinformatica - Dalla sequenza alla struttura delle proteine. Zanichelli 2011
· Andrew R. Leach, Molecular Modelling: Principles and Applications. Pearson - Prentice Hall 2001
Periodo
Primo semestre
Periodo
Primo semestre
Modalità di valutazione
Esame
Giudizio di valutazione
voto verbalizzato in trentesimi
Siti didattici
Docente/i
Ricevimento:
Su appuntamento
Dipartimento di Scienze Farmacologiche e Biomolecolari, Via Giuseppe Balzaretti, 9 - 20133 Milano
Ricevimento:
Su appuntamento
Dipartimento di Scienze Farmacologiche e Biomolecolari, Via Giuseppe Balzaretti, 9 - 20133 Milano