D1 - Knowledge and understanding.
At the end of the course the student will have acquired:
A good knowledge of the foundations of catalysis in organic reactions, in particular for reactions relevant to biological processes;
A good understanding of the general principles and specific characteristics of enzyme catalysis;
A detailed knowledge of the mechanisms of certain classes of enzyme reactions (hydrolysis, redox, C-C bond formation, substitutions and eliminations), with particular regard to the specific catalytic role of enzymes and coenzymes;
Understanding of the relationships between enzyme structure and catalytic activity and of the design strategies of enzyme inhibitors.
Further objectives are a good knowledge of RNA catalysis, of the main classes of enzyme mimics, and of immunochemistry fundamentals including bioconjugate techniques and the chemical aspects of vaccine development.
D2 - Applying knowledge and understanding.
At the end of the course the student should be able to:
Interpret the mechanism of an enzymatic reaction, in particular with regard to the catalytic role of the enzyme;
Use specific software for the 3D - visualisation of organic and biological molecules;
Find and retrieve information from the literature and from databases.
D3 - Making judgments.
At the end of the course, the student should be able to critically analyze the scientific literature regarding the mechanisms of enzyme reactions and, possibly, propose alternative hypotheses.
D4 - Communication Skills.
At the end of the course the student should be able to describe with a correct terminology the mechanism of an enzyme reaction, also using visual aids and visualization software.
D5 - Learning Skills.
During the course, the student should acquire the knowledge of concepts that will assist in the learning and understanding of subjects at the interface between chemistry and biology such as pharmaceutical chemistry, biochemistry, molecular biology, and biotechnology.

A good knowledge of organic chemistry and of the mechanism of organic reactions. Introductory knowledge on the structure and function of proteins.
Being familiar with the kinetic theory of organic reactions and with the fundamental concepts of thermodynamics.

Catalysis in Organic and Bioorganic Chemistry. Recognition and catalysis. Enzyme-substrate interactions. Enzyme catalysis: catalytic efficiency, specificity, selectivity and recognition. Bifunctional catalysis. Intramolecular catalysis. Specific and general acid-base catalysis. Brønsted equation. Nucleophilic catalysis. Electrophilic catalysis. Mechanisms in Enzyme Catalysis. Transferases: proteases, lipases and esterases, phosphatases and phosphodiesterases, glycosidases. ATP: ATPase and ATP synthase. Redox reactions: NAD-, FAD- and metal-dependent enzymes. CC bond formation: aldolases, squalene oxide cyclase, methylmalonyl CoA mutase, chorismate mutase. Nucleophilic substitutions and 1,2-eliminations. Catalytic RNA. Enzyme inhibitors. Immunichemical applications of bioorganic chemistry. Bioconjugates.

Catalysis in Chemistry and Enzymology
William P. Jencks
Dover, 1987.
ISBN-13 ‏ : ‎ 978-0486654607

Introduction to Enzyme and Coenzyme Chemistry
Author(s):T. D. H. Bugg
First published:29 June 2012
Print ISBN:9781119995951 |Online ISBN:9781118348970 |DOI:10.1002/9781118348970
Copyright © 2012 John Wiley & Sons, Ltd

Bioconjugate Techniques
G. Hermanson
Academic Press; 3rd edition (September 2, 2013)
ISBN-10 ‏ : ‎ 0123822394
ISBN-13 ‏ : ‎ 978-0123822390

Vaccine Development: From Concept to Clinic
Edited by A Krishna Prasad
Royal Society of Chemistry
Hardback ISBN: 978-1-78801-877-7
Publication date: 09 Nov 2022

INTRODUCTION
Catalyst definition. Kinetics and thermodynamics. Activation energy and Eyring equation.
The Michaelis Menten equation. Meaning of kcat and KM. Catalytic efficiency of enzymes.
Structure and properties (review). Non-proteinogenic amino acids. Post-translational modifications in proteins. Reactivity of the side chains. Acids, bases and nucleophiles.
The amide bond: peptides and proteins. Secondary and tertiary structure. Protein and enzyme structure.
CATALITIC EFFICIENCY
Recognition and catalysis. The lock and key model. Induced fit. Affinity for the transition state.
Enzyme-substrate interactions. Hydrogen bonds, non-covalent interactions.
Bifunctional catalysis: glucose mutarotation; ketosteroid isomerase.
Intramolecular catalysis. Effective molarity.
Substrate distorsion.
Specificity, selectivity and recognition.
ACID-BASE CATALYSIS
Specific and general acid-base catalysis. Mechanistic general acid-base catalysis. Examples: hydrolysis of esters, acetals and enoleters, α-halogenation of carbonyl compounds, aldol addition, condensation of carbonyl compounds with amines.
Brønsted equation: halogenation of ketones. Extensions of the equation: βnu and βlg; transesterifications.
Aspartyl proteases
NUCLEOPHILIC AND ELECTROPHILIC CATLYSIS
Nucleophilic catalysis: Williamson synthesis catalyzed by iodide, benzoin condensation, aldol addition, hydrolysis of esters catalyzed by tertiary amines.
Serine and cystein proteases
Electrophilic catalysis: Friedel-Crafts reactions; ring opening of epoxides; decarboxylation of β-keto acids; hydrolysis of aminoesters.
Metalloproteases
MECHANISMS OF ENZYME CATALYSIS
Hydrolysis and transfer reactions.
o Lipases and esterases; ACE inhibitors; interfacial activation; biocatalysis.
o Hydrolysis of phosphate esters. Phosphatases and phosphodiesterases.
o ATP and energy storage: biosynthesis of esters and amides; ATPase, ATP synthase, SAM.
o Glycosidase
Redox reactions .
o NAD-dependent enzymes: alcohol dehydrogenase.
o FAD-dependent enzymes: monooxygenase, glutathione reductase.
o Metal-dependent enzymes: cytochromes P-450.
Formation of C -C bonds.
o Via carbanions: class 1 and class 2 aldolases.
o Via carbocations: squalene oxide cyclase.
o Via radical reactions: methylmalonyl CoA mutase.
o Via pericyclic reactions: chorismate mutase.
Nucleophilic Substitutions and 1,2- eliminations.
o Haloalkane hydrolase
o Epoxide hydrolase
o Histidine ammonia lyase
Catalytic RNA: ribosome and ribozymes.
IMMUNOCHEMICAL APPLICATIONS
The immune system. Immunogenic bioconjugates. Bioorthogonal chemistry in bioconjugation. Innovative strategies for vaccine development. mRNA vaccines.

Lessons in the classroom and tutorials. Critical analysis of literature.
All the teaching materials, including exercises and problems, will be made available on Moodle and MS-Teams.

The teacher is available at the Department of Chemical and Pharmaceutical Sciences, building C11 room 339, phone +39 040 558 3920, fberti@units.it

Oral examination on the subjects discussed in the course. Short, in depth presentation on a specific subject, to be submitted by the week before the talk. Starting from the presentation, the exam includes at least three questions on its contents, aimed at verifying the level of developing reasoning by applying theoretical knowledge to the data presented. After this discussion, in the second part of the exam, the student will be asked to discuss at least one topic not related to the presentation. The final evaluation will derive from: - discussions and questions during classes (10%) - quality of the presentation (20%) - questions on the presentation (20%) - questions on other topics (50%) The final evaluation is formulated according to the following grid: Excellent (30 - 30 with honors): excellent knowledge of the subject, excellent command of language, the student shows excellent ability to apply the basic knowledge for interpretation of the topic presented. Very good (27 - 29): good knowledge of the topics, notable command of language; the student is able to correctly apply the basic knowledge. Good (24-26): good knowledge of the topics, fair command of language; the student shows an adequate ability to apply the basic knowledge. Satisfactory (21-23): the student does not show full mastery of the subject, although he/she has basic understanding of the topics; however, he/she shows sufficient command of language and sufficient ability to apply the principles. Sufficient (18-20): minimal knowledge of the subject and minimal use of technical language, limited ability to adequately apply the theoretical knowledge. Insufficient: the student does not possess an acceptable knowledge of the subject.

This course explores topics closely related to one or more goals of the United Nations 2030 Agenda for Sustainable Development (SDGs)