First cycle
degree courses
Second cycle
degree courses
Single cycle
degree courses
School of Medicine
PHARMACEUTICAL BIOTECHNOLOGIES
Course unit
ADVANCED REACTIVITY AND MODELLING
MEP5070478, A.A. 2017/18

Information concerning the students who enrolled in A.Y. 2017/18

Information on the course unit
Degree course Second cycle degree in
PHARMACEUTICAL BIOTECHNOLOGIES
ME2193, Degree course structure A.Y. 2015/16, A.Y. 2017/18
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Number of ECTS credits allocated 7.0
Type of assessment Mark
Course unit English denomination ADVANCED REACTIVITY AND MODELLING
Department of reference Department of Pharmaceutical and Pharmacological Sciences
Mandatory attendance
Language of instruction English
Branch PADOVA
Single Course unit The Course unit can be attended under the option Single Course unit attendance
Optional Course unit The Course unit can be chosen as Optional Course unit

Lecturers
Teacher in charge ANDREA SARTOREL CHIM/06
Other lecturers STEFANO MORO CHIM/08

ECTS: details
Type Scientific-Disciplinary Sector Credits allocated
Educational activities in elective or integrative disciplines CHIM/08 Pharmaceutical Chemistry 3.0
Core courses CHIM/06 Organic Chemistry 4.0

Mode of delivery (when and how)
Period Annual
Year 1st Year
Teaching method frontal

Organisation of didactics
Type of hours Credits Hours of
teaching
Hours of
Individual study
Shifts
Laboratory 1.0 15 10.0 No turn
Lecture 6.0 48 102.0 No turn

Calendar
Start of activities 02/10/2017
End of activities 15/06/2018

Syllabus
Prerequisites: basic organic chemistry
Target skills and knowledge: Module A: Comprehension of mechanisms and reactivity principles of the chemical transformations presented. Assimilation of the tools for the discussion of reactivity in organic chemistry transformations.
Module B: Interpret, compare and integrate data obtained from different structural biology techniques; Build a model from X-ray diffraction data; Access a range of structural data from leading public repositories; Critically assess the quality of data and models and select the most appropriate structures for your particular needs; use a variety of analysis tools to identify structural similarities that can help identify protein function; Understand the applicability of molecular docking and molecular dynamics simulation in a drug discovery process.
Examination methods: written examination
Assessment criteria: Module A: Students should be able to recognize and discuss the mechanisms of the reactions presented, and to apply the tools presented in the course to critically predict the reactivity of organic molecules.
Module B: Participants should critically assess the quality of protein crystallographic data and models, and gain expertise in the integration and visualisation of data from different techniques, thus enabling the analysis of protein structure data for functional relationships.
Course unit contents: Module A: Selectivity and performance are key features of organic reactions occurring in biological environment. The grand challenge of organic chemistry is to tame the reactivity-selectivity principle in artificial media. The fundamental principles of organic reactivity will be addressed with a close look to the enzymatic processes. Students will be guided to unveil the mechanistic details of key transformations by addressing the kinetics and thermodynamic requirements of selected case-studies in both artificial and biological media.
Reactive intermediates in organic chemistry. Carbocations, carbanions, carbenes and radicals. Mechanistic studies. Nucleophilic substitutions SN2, SN1 and SNi. Eliminations E1, E2 and E1cb. Enolates, Enamines, carbon-carbon bond formation. Carboxylic acid derivatives. Electrophilic aromatic substitution. Aromatic compounds. Heterocycles.
Module B
• Structural data analysis and repositories;
• Tools for model building, refinement and homology modeling;
• Tools and resources for drug discovery (molecular docking and molecular dynamics).
Module B aims to teach computational aspects of protein structure determination, validation and analysis. It will cover the background of different structural biology techniques and provide hands-on experience in building a model from X-ray diffraction data. The importance of protein structure to drug discovery will also be illustrated with sessions dedicated to small-molecules and antibodies as drug candidates.
Planned learning activities and teaching methods: frontal lessons
Additional notes about suggested reading: lecture notes
Textbooks (and optional supplementary readings)