Parcours Chemistry for life sciences 2e année

Course outline:

This course describes synthetic approaches and methods for: the synthesis of library of small[1]molecules, the assembly of peptide and analogs, the engineering of molecular conjugates of biomolecules, and the applications of that family of molecules in therapeutics, diagnostics and nanotechnologies (i.e. biosensors).

Details:

1/ Peptides and protein engineering

I.Structural aspects

II.Synthetic strategies (SPPS, fragment synthesis, native ligation)

III.Applications in vectorization (Monoclonal antibodies, cell-penetrating peptides, peptide ligands, nanoparticles)

IV.Antimicrobial peptides, toxins

V.Pseudopeptides

2/ Chemical ligation

I. The different reactions

II.Multiple chemoselective ligations

III.Installing bioorthogonal functionality into target biomolecules

IV.In vivo click chemistry

3/ Combinatorial chemistry

I. Drug Discovery

II.Synthetic strategies (combinatorial vs parallel synthesis; solid vs supported synthesis)

III.Dynamic Combinatorial Chemistry / Target guided synthesis

4/ Biosensors

I. Medicinal, environment and food safety applications

II.Biomolecules for molecular recognition

III.Chemical modifications for immobilization and transduction

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This teaching module focuses on the main principles used in bioinorganic chemistry: i) to understand and mimic the metal binding sites naturally found in biological systems, and ii) to anticipate potential interactions of toxic metals or metal-based drugs in living organisms. A first part will be dedicated to the behavior of metal complexes in biologically-relevant conditions. We will present the main analytical and spectroscopic tools useful to decipher the nature of the metal complexes both in abiotic compounds and proteins. In a second part, important metal active sites (on the catalytic, therapeutic and biological points of view) will be described in details. The last part deals with the concept of bioinspired chemistry. We will see how bioinorganic chemists design complexes that are able to mimic natural systems.

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This course will (i) provide advanced knowledges on biological therapeutic targets to facilitate understanding of projects at chemistry-biology interface, (ii) introduce current and innovative projects bringing together chemists and biologists, and (iii) give methodologies to effectively synthesize scientific oral presentation and publication.

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It is recognized that a large number of bioactive compounds are cyclic molecules containing one or several heteroatoms (N, O, S, etc…). In this course, the chemical properties of the most representative 6- and 5-membered-ring  types of heterocycles and the major methods used for their synthesis will be reviewed. Applications will be extended to more complex structures. Nomenclature rules will also be explained and examplified.

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Students will develop knowledge of the chemical development of a bioactive compound in the pharmaceutical or crop science industries, from milligrams to tons: how the discovery chemistry synthesis route evolves into a manufacturing process.

They will develop further skills in analyzing and communicating informations, working individually and in teams.

Course outline:

The chemical development of a bioactive compound is first addressed through an open discussion.

Students then work individually and in small teams to gather informations from selected publications in english. Their reports to the class allow all students to discover important aspects of chemical development.

The topic is later on presented extensively by professionals from the industry (lectures).

Tutorials dealing especially with the safety of chemical processes and the analysis of synthetic routes complete the course.

French is the teaching language.

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Exploration des relations entre structure chimique et propriétés pharmacologiques

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Course outline:

This course describes synthetic approaches and methods for: the synthesis of library of small[1]molecules, the assembly of peptide and analogs, the engineering of molecular conjugates of biomolecules, and the applications of that family of molecules in therapeutics, diagnostics and nanotechnologies (i.e. biosensors).

Details:

1/ Peptides and protein engineering

I.Structural aspects

II.Synthetic strategies (SPPS, fragment synthesis, native ligation)

III.Applications in vectorization (Monoclonal antibodies, cell-penetrating peptides, peptide ligands, nanoparticles)

IV.Antimicrobial peptides, toxins

V.Pseudopeptides

2/ Chemical ligation

I. The different reactions

II.Multiple chemoselective ligations

III.Installing bioorthogonal functionality into target biomolecules

IV.In vivo click chemistry

3/ Combinatorial chemistry

I. Drug Discovery

II.Synthetic strategies (combinatorial vs parallel synthesis; solid vs supported synthesis)

III.Dynamic Combinatorial Chemistry / Target guided synthesis

4/ Biosensors

I. Medicinal, environment and food safety applications

II.Biomolecules for molecular recognition

III.Chemical modifications for immobilization and transduction

Voir la page complète

This teaching module focuses on the main principles used in bioinorganic chemistry: i) to understand and mimic the metal binding sites naturally found in biological systems, and ii) to anticipate potential interactions of toxic metals or metal-based drugs in living organisms. A first part will be dedicated to the behavior of metal complexes in biologically-relevant conditions. We will present the main analytical and spectroscopic tools useful to decipher the nature of the metal complexes both in abiotic compounds and proteins. In a second part, important metal active sites (on the catalytic, therapeutic and biological points of view) will be described in details. The last part deals with the concept of bioinspired chemistry. We will see how bioinorganic chemists design complexes that are able to mimic natural systems.

Voir la page complète

This course will (i) provide advanced knowledges on biological therapeutic targets to facilitate understanding of projects at chemistry-biology interface, (ii) introduce current and innovative projects bringing together chemists and biologists, and (iii) give methodologies to effectively synthesize scientific oral presentation and publication.

Voir la page complète

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It is recognized that a large number of bioactive compounds are cyclic molecules containing one or several heteroatoms (N, O, S, etc…). In this course, the chemical properties of the most representative 6- and 5-membered-ring  types of heterocycles and the major methods used for their synthesis will be reviewed. Applications will be extended to more complex structures. Nomenclature rules will also be explained and examplified.

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Course outline:

Common modelling methods based on classical (MM, MD) and quantal (HF, DFT) approaches are addressed and their application are illustrated during lectures. Three computational labs are made to make students familiar with the application of these methods.

Details:

I. Lect1- Introduction: The potential energy surface
II. Lect2- Molecular Mechanics, Forcefield methods
III. Lab1- Forcefield methods, exploration of a potential energy surface
IV. Lect3- Ab initio methods, the self-consistent field, basis sets, density functional theory and applications
V. Lab2- ab initio methods: electron structure, reactivity
VI. Lect4- Molecular Dynamics simulations
VII. Lab3- Molecular Dynamics Simulations

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Green chemsitry is a major evolution in organic chemistry for more efficient, sustainable transformations while minimizing by-products, solvents and waste. In this course, the 12 principle of green chemistry will be presented and illustrated through dedicated chapters to: solvents, catalysis, biotransformation, flow chemistry, organocatalysis and multicomponent and cascade reactions.

Details:

I – Introduction: History, E-factor, 12 principles
II- Solvents: greener solvent, no solvent, water, supercritical CO2, Ionic liquids,
III- Biocatalysis – Biomass
IV- Solids supported reaction/reagents, flow chemistry
V- Microwaves
VI- Multicomponent and cascade reactions
VII- Organocatalysis

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Course outline

The lectures present the basic methodology and some advanced techniques used for high throughput in vitro small molecule drug discovery. The principles and statistical methods used for assay optimization and validation will also be explained.

I. Molecular biology, Biochemistry and Protein expression

II. Proteomic analysis; Mass spectrometry

III. Lab-chips and Cell-chips

IV. Structural biology: Crystallogenesis and Crystallization; RMN

V. Combinatory chemistry

Format of exams:  Oral exam (at the end of December) and Research project (at the beginning of January)

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The course will present practical and theoretical aspects of the classical approaches used to determine the structure of macromolecules by X-ray crystallography and Nuclear Magnetic Resonance spectroscopy. The program of this course is described below:

  Part I - Crystallography - 20h

• Crystallization techniques                                                                            
• Crystal symmetry and space groups                                                                      
• Diffraction                                                                                                    
• Structure factors, reciprocal space etc                                                      
• Tutorial: Data treatment                                                                                          
• Phasing – MIR, SAD, MAD                                                                        
• Molecular replacement, crystallographic symmetry                                              
• Tutorial: MAD Phasing                                                                                              
• Tutorial: Molecular replacement                                                                             
• Refinement                                                                                                  
• Tutorial: Model building and refinement                                                                  
• Practical lab: Crystallization on a PSB platform                                                                 
• Practical lab: X-ray data collection on a ESRF beamline                                                  

    Part II – Nuclear Magnetic Resonance-20h

• NMR principles: active nuclei, magnetic field, radiofrequency excitation,
             return to equilibrium                                                                                     
• NMR observables in the spectra of biomolecules (chem. shift, scalar
             couplings,  linewidth)                                                                        
• NMR observables: measurement                                                               
• Practical lab on IBS-NMR platform: data collection
• The steps to structure determination: sample preparation, isotopic labeling
• The steps to structure determination: assignment   
• The steps to structure determination: extraction of structural parameters 
• Tutorial: Data analysis                                                                                 
• Structure calculation: principles                                                                              
• Practical lab: Protein structure calculation                                                  

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Exploration des relations entre structure chimique et propriétés pharmacologiques

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Cette unité d’enseignement de 3 ECTS est enseignée en Français et est divisée en trois grandes parties : Gestion de projet, Propriété industrielle, Plans d’expérience.

Gestion de projet

Le cours se compose de deux parties :

1. Communication qui est la poursuite de l’UE Communication tools pour approfondir la connaissance de soi et savoir se présenter lors d’un entretien de recrutement

2. Gestion de projet: Initiation à la gestion entrepreneurial permettant d’avoir un aperçu des outils de gestion de projets, des bases en gestion
et en entrepreneuriat.

Propriété industrielle

Résumé du cours : principes fondamentaux des droits de propriété intellectuelle : conditions, effets et exceptions des droits de brevet, savoir-faire, marque, dessin et modèle, obtentions végétales, topographie des semi-conducteurs, de la contrefaçon.

Détails :
Droit du brevet : conditions de fond, de forme pour obtention du titre. Effets et limites du brevet, national et européen.
Droit de la marque : conditions de fond, de forme pour obtention du titre. Effets et limites de la marque, nationale et européenne.
Droit des dessins et modèles: conditions de fond, de forme pour obtention du titre. Effets et limites du titre, national et européen.
Principes des topographies de semi-conducteur, obtention végétales, droit d’auteur.
L’action en contrefaçon : la preuve, les démarches, les résultats.

Plans d’expériences

Résumé du cours : Le cours traite des principaux plans d’expériences habituellement rencontrés (plan factoriels complet, plan factoriels fractionnaire, plans pour surface de réponses). L’analyse statistique des plans d’expériences sera également abordée.

Détails : Le cours est constitué des 4 items suivant :

• Les plans factoriels complets
• Les plans factoriels fractionnaires
• Plan pour surface de réponses
• Traitement statistique des plans d’expériences

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The aim of the M2 internship is to put all the theoretical and practical skills acquired by the students since their Bachelor's degrees into practice as they take part in a research or R&D project in a laboratory (program R) or company (program P). The students will be entrusted with a clearly identified mission, and they will be responsible, firstly, for its completion, and secondly, for the presentation of the methods implemented and results obtained in a written report and through one or more oral presentations.

L'objet du stage de Master 2 est de recruter l'ensemble des connaissances théoriques et pratiques acquises par l'étudiant depuis la Licence pour participer à un projet de recherche ou de R&D dans un laboratoire (parcours R) ou une entreprise (parcours P). Une mission clairement identifiée sera confiée au stagiaire, qui sera en charge d'une part de son accomplissement, d'autre part de la présentation des méthodes mises en oeuvres et des résultats obtenus dans un rapport écrit et via une ou des présentations orales.

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The syllabus of the English course in M2 aims at enabling students to validate 3 competences that will be essential for their working life or for their doctoral studies in the future, at the B2 level: 1°) CAN give a clear presentation on a familiar topic, and CAN answer predictable or factual questions 2°) CAN find relevant information and essential points in written texts 3°) CAN make simple notes that are of reasonable use for essay or revision purposes, capturing most important points." (CEF, appendix D). Reading comprehension can be validated in M1. The course contents are linked to the students' fields of studies.

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Choix d'un ETC si niveau anglais >= B2

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The aim of the M2 internship is to put all the theoretical and practical skills acquired by the students since their Bachelor's degrees into practice as they take part in a research or R&D project in a laboratory (program R) or company (program P). The students will be entrusted with a clearly identified mission, and they will be responsible, firstly, for its completion, and secondly, for the presentation of the methods implemented and results obtained in a written report and through one or more oral presentations.

L'objet du stage de Master 2 est de recruter l'ensemble des connaissances théoriques et pratiques acquises par l'étudiant depuis la Licence pour participer à un projet de recherche ou de R&D dans un laboratoire (parcours R) ou une entreprise (parcours P). Une mission clairement identifiée sera confiée au stagiaire, qui sera en charge d'une part de son accomplissement, d'autre part de la présentation des méthodes mises en oeuvres et des résultats obtenus dans un rapport écrit et via une ou des présentations orales.

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The syllabus of the English course in M2 aims at enabling students to validate 3 competences that will be essential for their working life or for their doctoral studies in the future, at the B2 level: 1°) CAN give a clear presentation on a familiar topic, and CAN answer predictable or factual questions 2°) CAN find relevant information and essential points in written texts 3°) CAN make simple notes that are of reasonable use for essay or revision purposes, capturing most important points." (CEF, appendix D). Reading comprehension can be validated in M1. The course contents are linked to the students' fields of studies.

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Choix d'un ETC si niveau anglais >= B2

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